Liverpool conceded top spot in Group A to Europa League opponents Anzhi Makhachkala after a 1-0 defeat in Moscow.
Giant striker Lacina Traore scored a brilliant individual goal as the visitors switched off seconds before half-time.
The result, the Reds' first-ever away defeat in the group stage and only their third loss in 22 European matches, allowed the Russian club to assume pole position.
Raul Bobadilla's fourth goal against Udinese in two games and second-half strikes from Alexander Farnerud and Raphael Nuzzolo inspired Young Boys to a shock 3-2 win over the Italian side.
Martin Rueda's men stunned Udinese on home soil 3-1 two weeks ago thanks to Bobadilla's treble and the Argentinian was on target to set the Swiss outfit on their way before veteran striker Antonio Di Natale levelled early in the second half - seconds after he had missed from the penalty spot.
However, the visitors re-established their lead through Farnerud and Nuzzolo before Diego Fabbrini set up a tense finale. The result sent Young Boys up to third in the group, level on six points alongside Liverpool, while Udinese prop up the table.
Uruguay striker Edinson Cavani scored all four goals - including two in the dying moments - to lead his Napoli side to a memorable 4-2 win over Group F leaders Dnipro.
In the build-up to Thursday's game, Partenopei boss Walter Mazzarri had made a point of denying he was in charge of a one-man team, but his star man did his best to contradict him with a sterling performance.
Cavani opened the scoring after just seven minutes, and when his side slipped behind following strikes from Artem Fedetskiy and Roman Zozulya, he hauled them back with goals after 77, 88 and 93 minutes.
AIK claimed their first win in Group F - 1-0 at the expense of Eredivisie side PSV Eindhoven.
Mohamed Bangura's first-half strike was all that separated the two sides at Rasunda, with the Swedish club joining their opponents on four points in the table.
Shola Ameobi's 14th European goal kept Newcastle's campaign on track as they drew 2-2 on an eventful evening against Club Brugge.
The 31-year-old struck from younger brother Sammy's 43rd-minute pass two minutes after Vurnon Anita had dispatched a sweet volley to cancel out the 2-0 lead Brugge had been handed on a plate during an awful start by the visitors.
The Belgians went ahead with 14th minutes gone when Ivan Trickovski embarrassed skipper Fabricio Coloccini to register the first Group D goal conceded by Newcastle, and Jesper Jorgensen doubled their advantage within five minutes with Alan Pardew's men simply not at the races.
However, a side featuring eight changes to the one which ran out at Liverpool on Sunday managed to summon up a commendable response to take a point which means they remain at the top of the group.
Bordeaux moved to within a point of Newcastle after a solitary David Bellion goal guided the French side to a narrow 1-0 victory over Maritimo .
Bellion headed home in the 16th minute to give the Ligue 1 team all three poins and the margin of victory could have been greater with Carlos Henrique hitting the post and their Portuguese visitors creating little of note, although they did have a late goal disallowed for offside.
Academica snapped Atletico Madrid's 16-game winning run in European competitions thanks to a goal either side of half-time by Wilson Eduardo in a 2-0 victory.
Diego Simeone finally paid for resting his stars in the Europa League as the Portuguese side taught the holders a lesson in taking their chances.
Eduardo pounced on Marinho's excellent ball in to slide past Sergio Asenjo on 28 minutes and the same player sealed the points from the penalty spot 21 minutes from time after Jorge Pulido had brought down Salim Cisse. Victory keeps Academica's hopes of qualification alive as they move on to four points.
Daniel Kolar scored twice as Viktoria Plzen boosted their hopes of qualifying for the knockout stages with an emphatic 4-0 win over Hapoel Tel Aviv.
Kolar scored once in each half and further goals from David Stipek and Marek Bakos virtually guaranteed Plzen's progress as they moved level with Atletico Madrid at the top of Group B. Meanwhile the result guaranteed elimination for the Israelis, who continue to languish at the bottom of the group with just a single point from their opening four games.
Jermain Defoe responded to his England snub by scoring a superb hat-trick that put Tottenham's European campaign back on track.
Just nine hours after he was left out of Roy Hodgson's Three Lions squad, the Spurs striker put in a top-class performance in the 3-1 victory over Slovenian side NK Maribor, scoring all three goals to move Tottenham up to second in Group J with two matches to go
Lazio lifted their heads before this Sunday's derby against Roma as they consolidated their position atop Group J with a comfortable 3-0 victory over Panathinaikos.
Bouncing back from last weekend's shock 4-0 loss to Catania, Lazio boosted their confidence behind two goals from Libor Kozak and a third strike from Sergio Floccari. The win moves Lazio on to eight points, two clear of Spurs at the top of the group.
Juan Arango's injury-time equaliser kept Marseille and Borussia Monchengladbach locked together in the battle to escape Group C as the Germans nicked a point from a see-saw 2-2 draw at the Stade Velodrome.
Moments after Marseille's Loic Remy had headed against the crossbar, it was Gladbach who struck first through Mike Hanke. Joey Barton's goal direct from a corner levelled it seven minutes into the second half and Jordan Ayew turned the game on its head by giving Marseille a 67th-minute lead as their pressure told.
But Marseille were denied the three points when Arango fired home in the 93rd minute for a somewhat fortunate Gladbach side.
Fenerbahce are almost assured of reaching the knockout stages following a comfortable 2-0 home win against 10-man AEL Limassol.
First-half goals from Dirk Kuyt and Moussa Sow ensured the hosts were able to coast to victory in summer signing Raul Meireles' return to the first team from injury, while AEL's misery was compunded by a straight red card for Edwin Ouon - the scorer of their only goal in the group so far - following his professional foul on Sow with 20 minutes left.
Last season's finalists Athletic Bilbao were all but eliminated from the competition as Lyon kept up their 100% record with a 3-2 win at San Mames.
First-half goals from Baftimbi Gomis and Yoann Gourcuff put the French side in a commanding position but Athletic roared back after the break and were level within nine minutes of the restart thanks to Ander Herrera's finish from close range and an Aritz Aduriz penalty.
However, rather than building on that momentum the hosts conceded the winner eight minutes later as Gueida Fofana got to the byline and cut the ball back for Alexandre Lacazette to fire in a wonderful effort from the edge of the area. A third defeat in four leaves Athletic bottom of the group with just the one point and needing to win their last two games and hope Sparta Prague also lose against Lyon to have any chance of making the last 32.
Sparta Prague strengthened their grip on second place in Group I with a 1-1 draw at Hapoel Kiryat Shmona. The Israeli hosts took an early lead through Darko Tasevski before Leonard Kweuke struck for Sparta. The draw sees Sparta retain their five-point advantage over their rivals. Szabolcs Huszti kept his nerve to fire home a late penalty and secure a 3-2 victory and Hannover's qualification for the knockout stages at the expense of nine-man Helsingborg.
Huszti scored an 88th-minute spot-kick whose award for a foul on Artur Sobiech so enraged the visitors they had both Peter Larsson and Walid Atta sent off for protesting. And the goal proved enough for the Germans to guarantee their progression.
Rodrigo Palacio bagged a brace to help Inter Milan qualify for the knockout stage with a comfortable 3-1 win at Partizan Belgrade.
Rubin Kazan's 1-0 victory over Neftchi meant Inter needed just a point in the Serbian capital to reach the knockout rounds although they were indebted to keeper Samir Handanovic for two world-class saves from Ivan Ivanov in the first half.
And Inter rewarded their keeper as Palacio netted twice and Fredy Guarin completed the triumph before Nemanja Tomic grabbed an injury-time consolation for Partizan.
Levante moved a step closer to progressing to the last 32 with a stubborn defensive performance to claim a 0-0 draw away to FC Twente.
Bayer Leverkusen booked their place in the knockout stages with an emphatic 3-0 home win over rock-bottom Rapid Vienna.
The Germans led after just three minutes, through Jens Hegeler, but had to withstand a valiant Rapid before making the game safe in the space of eight second-half minutes.
Andre Schurrle volleyed home his side's second on 58 minutes before Manuel Friedrich got on the scoresheet moments later. Victory ensured both teams had sealed their place in the last-32 with two games to spare.
Metalist Kharkiv remained level on points with Bayer Leverkusen following a 3-1 victory over Rosenborg.
Freda Taison had given the hosts an ideal start with a goal in the fourth minute and they were clearly the better side in the first half.
However, Rosenborg equalised through Borek Dockal three minutes before half-time. It was a far more even contest after the break but the Ukrainians edged ahead through Cleiton Xavier before Juan Manuel Torres sealed victory in injury time.
Steaua Bucuresti all but secured their passage from Group E with a 2-1 victory over Molde in Norway.
First-half goals from Alexandru Chipciu and Iasmin Latovlevici did the job for Laurentiu Reghecampf's side and though Daniel Chukwa got one back for the hosts 10 minutes into the second half, they rarely threatened an equaliser and Steaua are now six points clear at the top of the group.
Stuttgart stormed into the qualification places in Group E with their first win of the campaign, 2-0 at Danish league leaders FC Copenhagen.
Vedad Ibisevic and Martin Harnik scored in the final quarter to seal a win that owed also to goalkeeper Sven Ulreich's heroics in the opening 45 minutes.
Sporting were seconds away from holding on to victory in their Group G clash against Genk, despite playing for half an hour with 10 men in Lisbon.
The hosts had Stijn Schaars sent off for a second yellow card just before the hour mark but rallied to take the lead through Ricky van Wolfswinkel just six minutes later. They held on their advantage until the first minute of injury-time when Glynor Plet headed the Belgian side level and the game finished 1-1.
A share of the spoils is of little use to Sporting, who sit bottom on group on two points, but Genk saw their hopes of topping the table boosted as they moved two clear with eight points from four games.
A goal by Marco Streller 10 minutes from time was enough to guide Basel to their first victory in this year's Europa League as they claimed a deserved 1-0 win over Videoton in Group G.