Zulte-Waregem missed out on qualification for the Europa League knockout stage after a 2-0 defeat by Group D leaders Rubin Kazan.
The Belgian Pro League side only needed a point to make sure of their qualification and finish second in the group behind Rubin, who topped the pile with 14 points.
However, Bebras Natcho's 79th-minute penalty and Jose Salomon Rondon's late score ended that hope, as Maribor leapt into the last 32 from the bottom of their group thanks to a 2-1 win over Wigan.
Yann M'Vila had a speculative effort for Rubin in the 12th minute when he fired wide from 25 yards before Natcho went closer for the visitors when his 18-yard volley was caught by goalkeeper Sammy Bossut.
Thorgan Hazard's corner just before the half-hour mark gave Frederic Duplus a chance for Zulte but the defender shot wide, before Hazard hit the wall from a 20-yard free-kick.
The midfielder blasted the ball over the bar early in the second half as Ivan Marcano sent a long-range effort wide at the other end just before the hour mark.
Chris Mavinga also fired wide for the visitors as neither side seemed to have the capacity to break the deadlock in a largely frustrating game.
But that all changed as the match entered the final quarter when Duplus fouled Sergey Kisliak to give away a penalty, which Natcho converted.
Salomon Rondon made sure of a perfect finish to the group stages for his side with an 86th-minute strike from the middle of the box to leave Zulte tumbling out of the tournament despite a flurry of late shots from the home side.