LATICS left it late - but penalty king Jordi Gomez fired them to a seventh successive victory against the Owls.
Gomez set Latics on their way to the FA Cup semi-finals with the opening goal from 12 yards at Manchester City on Sunday.
And he was once again the man on the spot when James Perch was felled with just three minutes to go.
Goalkeeper Damian Martinez guessed right, but the ball had enough elevation and pace to find the net - and keep Latics on the promotion track.
Uwe Rosler’s side moved back up to seventh, a point behind fifth-placed Nottingham Forest with two games in hand.
Latics had earlier dodged a bullet in the first half when they conceded a penalty of their own.
Jacques Maghoma toed the ball past Ali Al Habsi, who brought down the Wednesday man.
Referee Andy Haines elected only to brandish yellow when another official may have sent off Al Habsi.
And the goalkeeper rubbed salt into the Wednesday wounds by diving to his right and keeping out Leon Best’s penalty.
Latics always looked the side more likely to win it, but the closest they came was Callum McManaman firing just past the post - before Gomez’s late, late show.
FOR A FULL REPORT, REACTION AND PICTURES, SEE THURSDAY’S WIGAN EVENING POST.