Goals either side of half time by Jacob Murphy and Kieffer Moore looked to have ensured that Wigan and Wednesday would share the spoils on a freezing night over the Pennines.
But Jamal Lowe had the final word, heading a late, late winner to give the Latics a ray of light at the foot of the Championship.
The hosts enjoyed more of the ball and the chances to chalk up just a second win in 17 games and they were overall good value for the points.
For Wednesday it was a night to forget and a furious Garry Monk has already demanded a significant improvement when his side host Millwall on Saturday.
Wigan began brightly although they had to wait until midway through the first half to fashion an opening.
Lee Evans found Antonee Robinson charging towards goal down the inside left channel but the defender’s shot was high and wide.
Dominic Iorfa timed his tackle perfectly to thwart Joe Gelhardt moments later as the Latics showed plenty of intent on the offensive.
But Wednesday came into life on the half-hour mark to hit the front. Moments after Murphy burst into the area and dragged tamely across goal, the in-form winger made amends in style.
Barry Bannan picked out the marauding Morgan Fox, whose cross was pinpoint and emphatically headed home by the onrushing Murphy.
Wigan responded with skipper Samy Morsy unleashing a speculative effort from all of 30 yards that Cameron Dawson palmed to safety before Fox brought the first 45 to a close, narrowly firing wide on the half volley.
The hosts started the second period on the front foot, playing neat possession football and this time got their reward 10 minutes in.
Gelhardt took a quick free kick that found Moore deep in the area and the striker drilled hard and low past Dawson to level the scores.
The same two players combined almost straight from the restart to give Wednesday a scare as Moore’s glanced header was deflected wide by Moses Odubajo at the back post.
The Latics stayed in the driving seat and Cedric Kipre might have done better after racing into the box on the angle but his tame shot was comfortably gathered by Dawson.
The Wednesday keeper then denied substitute Michael Jacobs and Morsy again tried his luck from distance but scooped over the bar.
Still the Latics pressed as Wednesday were forced back and Paul Cook’s side got their reward a minute from time.
Robinson crossed accurately from the left flank, Moore nodded on and Lowe headed over the advancing Dawson to seal three vital points.
Wednesday: Dawson, Odubajo, Iorfa, Börner, Fox (Lees 51), Murphy, Bannan, Pelupessy, Harris (Reach 71), Winnall (Rhodes 58), Nuhiu