It was a tale of two penalties at the DW Stadium as Wigan broke Sheffield Wednesday’s stubborn resistance by grabbing the only goal of the game with a late spot kick.
Leon Best missed the chance to give the Owls a first half lead from the penalty spot after Jacques Maghoma had been hauled down by Wigan goalkeeper Al Habsi.
And having weathered a storm for so long after that, defending superbly at times, all their hard work was undone in the 88th minute when Caolan Lavery brought down James Perch.
Jordi Gomez stepped up to plant the winner past Damian Martinez.
Stuart Gray made three changes to the side which turned in a disappointing display in losing to Yeovil on Saturday.
Out went Gardner and the suspended Sam Hutchinson with Lewis Buxton and Adedeji Oshilaja coming in, while Chris Maguire dropped to the bench and young striker Caolan Lavery earns a start.
As expected, Chris Kirkland wasn’t fit enough to play, with Damian Martinez keeping his place in goal.
David Prutton, who hasn’t played since September after undergoing ankle surgery, was named amongst the Owls substitutes.
The Owls had been battling well in an entertaining yet tight encounter where neither side had really threatened to score.
However, Wednesday were given the perfect chance to do so on 35 minutes when Maghoma rounded Al Habsi and was hauled down, with the travelling Owls fans appealing for a red card.
The Latics keeper remained on the pitch though and to add insult to injury saved from Best.
There were few chances of note early on in the game but the match sparked into life after that missed penalty and it was the home side who were then doing much of the pressing.
They came closest on 42 minutes when Ryan Tunnicliffe let fly with a stunning drive which forced a great save from Martinez.
And from the corner Martinez saved again as he tipped away Boyce’s header from a Gomez cross.
After the break Wednesday started well and though again, not putting too much pressure on goal, aside from Lavery winning a corner which eventually came to nothing, they weren’t allowing Wigan to come forward and the home fans were becoming frustrated.
In a bid to unlock the hard-working Owls midfield and backline, Wigan boss Uwe Rosler made a double substution on 53 minutes with James McArthur replaced by Nick Powell and Martyn Waghorn coming off for Callum McManaman.
That switch helped the Latics up the tempo and they began asking more questions of the Wednesday defence.
On the hour mark Wigan had their best chance when Gomez’s ball into the box found Perch but his header was cleared off the line.
Wednesday then made a double substitution of their own a minute later with Maghoma coming off for Maguire and Prutton replacing Oshilaja.
If Wigan were to score it would likely come from a set piece as Gomez’s deliveries were always sent into dangerous areas, however, to their credit, Wednesday’s defenders were equal to everything that came their way.
Fortune replaced James McClean on 72 minutes for Wigan and on 75 minutes Atdhe Nuhiu came on for Best as both sides made their final substitutions.
With the game heading towards the latter stages, Wigan had two great chances to break the deadlock in quick succession.
First, substitutes Fortune and McManaman combine on 79 minutes with the latter shooting wide when he perhaps whould have scored, then a minute later Gomez ran at the Wednesday defence and upon getting a sight on gola, he too hit his effort wide.
Liam Palmer hit the side-netting on 82 minutes in a rare attacking foray for the Owls but soon after, back at the other end McManaman fed Fortune and it was his turn to miss the target.
Then came the winner as Lavery upended Perch and Gomez buried the spot kick to claim all three points for the Latics.
It was tough on Wednesday. Wigan had the majority of the play but the visitors had defended well and their hard work looked deserving of a point, while they will also look to the fact that Al Habsi could and perhaps should have been sent off for his challenge on Maghoma which brought about the penalty, missed by Best.
Wigan: Al Habsi, McClean, Gomez, McArthur, Boyce, Beausejour, Perch, Barnett, Maynard, Tunnicliffe, Waghorn. Subs: Carson, Crainey, McEachran, McManaman, Powell, Ramis, Fortune
Sheffield Wednesday: Martinez, Buxton, Helan, Oshilaja, Onyewu, Loovens, Palmer, Coke, Best, Lavery, Maghoma: Subs: Johnson, Prutton, Davies, Maguire, Afobe, Llera, Nuhiu
Referee: Andy Haines