Real Betis saw Lyon leapfrog them to the top of Group I with a 1-0 win at Stade Gerland on Thursday, but both teams were able to celebrate a place in the last 32 of the Europa League.
Substitute Bafetimbi Gomis finished off a good move to net the only goal of the game in the 66th minute as Lyon inflicted a first group defeat on Betis to move into first place.
However, third-placed Vitoria Guimaraes are now unable to pip Betis to second spot after being held to a goalless draw at Rijeka.
That was the good news for Betis, but it may not do much to ease the pressure on coach Pepe Mel, whose side have had an awful start to their Primera Division campaign and lie bottom of the table with only nine points from 14 games. They also suffered a 4-0 derby mauling at the hands of arch-rivals Sevilla at the weekend.
Betis have found Europe a happy distraction from their domestic woes, and would have guaranteed themselves a first-placed finish with a win in France.
Both sides had chances to take the lead during a goalless first half, with Lyon going the closest when Alexandre Lacazette squeezed a shot past Stephan Andersen only for Betis to scramble it off the line.
Betis' best opening of the game came on the hour mark, and should have seen them take the lead.
Samuel Umtiti's terrible attempted back-pass was intercepted by Chuli but, after taking the ball away from Lyon goalkeeper Remy Vercoutre, he could only fire against the near post with the goal at his mercy.
That proved a costly miss as, six minutes later, Lyon netted the match-winning goal.
Yoann Gourcuff's one-two with Lacazette ripped open the Betis defence and Gourcuff rolled the ball across the area for Gomis to tap into a gaping net.
Betis pushed for a late equaliser, but Markus Steinhofer saw a shot deflected wide before Chuli's stoppage-time header was tipped over by Vercoutre as Lyon held on for the win.