Wednesday gave as good as they got for long periods against a lacklustre Latics outfit.
And they only had themselves to blame for not going into the break a goal to the good after Leon Best had a penalty of his own saved by Ali Al Habsi.
The home side picked up their game after the break, but it looked like it was going to be one of those days when substitute Callum McManaman fired inches wide of the post inside the final quarter.
But Wigan never gave up hope of breaking the deadlock, and were rewarded when Caolan Lavery tripped James Perch inside the box with 87 minutes on the clock.
And Gomez scored his second goal in the space of three days to lift Latics to seventh place, with two games still in hand.
Wigan had created a couple of chances inside the opening stages to go ahead, both opportunities stemming from the left.
First Jean Beausejour opted not to shoot when Damian Martinez had advanced off his line, instead playing the ball inside towards Nicky Maynard.
The striker's touch was poor and the ball fell to Martyn Waghorn, whose shot was saved by Martinez, who had recovered his position.
Then James McClean seemed to get caught between shooting for goal and playing the ball across to Maynard at the far post.
His drilled effort fizzed past the far post, with too much pace for Maynard to react and get his toe to the ball.
Liam Palmer fired Wednesday's fight sight of goal over the top, with Best doing likewise moments later.
The Owls then squandered an even better opportunity 10 minutes before the break, when they were awarded a penalty.
Jacques Maghoma raced through and was taken out by Al Habsi as he tried to round the goalkeeper.
Referee Andy Haines decided to only caution the goalkeeper when other officials may well have brandished red.
And Al Habsi took full advantage by reading Best's penalty and pulling off a fine save diving to his right.
Wigan ended the half on top with Ryan Tunnicliffe having a shot saved and Emmerson Boyce seeing a header tipped round the post.
But it just was not clicking for the home side, who made a double change at the start of the second period with Nick Powell and McManaman entering the fray.
Powell was immediately into the action, freeing McClean down the only, only for the winger's delivery to find only the goalkeeper's hands.
That was McClean's final contribution before he was replaced by Marc-Antoine Fortune, who almost created the opening goal for McManaman.
The ball to the winger was inch-perfect, but McManaman's radar was slightly off and the shot drifted inches past the far post.
But Wigan were not to be denied, and they were awarded a penalty with just three minutes remaining when Perch was felled inside the box by Lavery.
Gomez, who had opened the scoring from the spot in Wigan's victory over Manchester City at the Etihad on Sunday, placed the ball, and Martinez could not get near the excellently-executed effort.