Leon Barnett put Owen Coyle's men in front early on after a corner scramble but Chelsea loanee Thorgan Hazard levelled matters shortly before the break and the hosts were vexed
Leon Barnett put the hosts ahead early on, brilliantly volleying home from the edge of the penalty area after a Jordi Gomez miscue.
An open first half ended even, though, young Wigan goalkeeper Lee Nicholls spilling an effort from Thorgan Hazard over his own goal line.
The hosts looked like the only team likely to score in the second period but Junior Malanda slammed home an 88th-minute winner to move the Belgians second in Group D with one game to play.
|By Jamie Dunn
Well, that was about as open a game as you could hope to see. Wigan desperately wanted to tie up a place in the Europa League knockout stages and it was evident in the way that they played but Zulte-Waregem proved themselves more than capable on the counter.
Lee Nicholls's unfortunate mistake gave the visitors a way back into the game after Leon Barnett's opener and a touch of class at the end from Bernard Malanda means that Owen Coyle's side have to go to Maribor and win.
And, of course, even then it might not be enough.
Owen Coyle made six changes from Saturday's 1-0 defeat to Brighton and Hove Albion, Manchester United loanee Nick Powell starting at the head of Wigan's attack with Jordi Gomez supporting. Waregem came into the clash on the back of a six-game unbeaten run but still made three alterations from their weekend win over Mechelen.
The hosts were ahead after just seven minutes as Callum McManaman and Gomez worked a short corner routine, only for the Spaniard to mis-hit his effort. However, the ball fell perfectly for Barnett, who slammed home his fourth goal of the season.
Within 10 minutes of the opener, McManaman almost doubled the lead and Waregem midfielder Sven Kums scuffed wide after electric build-up play from Frederic Duplus on the left.
James McClean ended a strong run with a shot from the left channel that visiting keeper Sammy Bossut saved well, although the Irishman had better options centrally.
And Bossut's sharpness was rewarded in part through an error by his opposite number as the visitors pounced on an error from James McArthur to drive up the field. The ball eventually found Hazard, whose firm effort was straight at Nicholls but the 21-year-old was caught in two minds and could only drop the ball over the line.
Powell stung Bossut's palms with a well-struck shot on the hour, while Nicholls reacted well to palm Hazard's deflected free kick behind eight minutes later as the sides firmed up after the break.
McArthur drilled a 20-yard shot wide with 10 minutes on the clock as the hosts pushed for a winner that looked as though it would fail to materialise.
But Malanda got on the end of fellow substitute Idrissa Sylla's cutback and lashed an unstoppable effort past Nicholls to deflate the home crowd and put Waregem in the driving seat for a spot in the next phase.