Wednesday suffered a cruel defeat on a night of two vital penalty incidents at the DW Stadium last night.
The Owls were left cursing referee Andy Haines after he refused to send off Wigan keeper Ali Al Habsi for bringing down Jacques Maghoma in the first half.
Then a dubious decision gave the Latics the spot-kick from which midfielder Jordi Gomez hit an 88th-minute winner.
It was hard on Wednesday after they bounced back from the flop at Yeovil to deliver a disciplined and workmanlike performance that deserved at least a point.
Tyne and Wear official Haines has sent off nine players this season but only he booked Al Habsi after he felled Maghoma when the forward was through on goal.
It looked an obvious red-card offence for denying a goalscoring opportunity, as well as being a definite penalty.
But Haines produced a yellow, and though Al Habsi made a good save from Leon Best’s 37th-minute spot-kick, he should not have been on the field.
Wigan’s penalty was given for a challenge by Caolan Lavery on James Perch after the Wigan right-back seemed to go down very easily.
Stuart Gray made changes. Lewis Buxton had his first appearance of the boss’s reign - the last having been the 2-0 defeat at Blackpool in November which was followed by Dave Jones’ sacking.
Adedeji Oshilaja was playing the final game of his month on loan from Cardiff and his only other outing was in the 3-0 home defeat by Wigan a month ago.
The other change saw the return of Lavery.
Gary Gardner and Sam Hutchinson both missed out on the final match of their loan spells, with the former not in the 18 and the latter suspended after his sending-off at Yeovil on Saturday.
Chris Maguire was demoted to the bench but David Prutton would be glad to be there after his long lay-off with an ankle injury.
Oshilaja, signed from Cardiff as a centre-half who could play in other positions, was given a holding midfield role.
Liam Palmer and Giles Coke were in central midfield, while Maghoma and Lavery supported Best on the left and right respectively but tracked back when necessary.
Gray will have been trying to match the sort of midfleld strength that Wigan showed at Hillsborough.
The Latics’ seven changes last night to the side that started the FA Cup win against Manchester City did not mean they were taking Wednesday lightly - it was almost the same line-up that played in the club’s previous league game, a 4-1 win at Forest.
Wigan’s first threats came down the left wing, firstly in tempting Damian Martinez from his goal only for striker Martyn Waghorn to shoot tamely at the keeper.
Then James McClean got in behind Buxton and hammered a ball low across goal, with a teammate narrowly failing to connect.
Wednesday were solid after that, for the first half hour, and Buxton made two canny challenges on the winger.
They were also promising on the break at times and it was their best attacking move yet that led to the penalty.
Best slipped a pass through to Maghoma and as he touched the ball past Al Habsi in a central position inside the box he was sent flying by the keeper.
It was a definite penalty and it should haved been a red card but ref Andy Haines showed only a yellow to Al Habsi as Maghoma received treatment.
To add insult to injury, the keeper guessed correctly in diving to his right to beat away Best’s spot kick.
As if inspired by that escape, Wigan surged forward for midfielder Ryan Tunnicliffe and centre-half Emmerson Boyce to test Martinez with a 25-yard strike and a downward header.
But the Owls deserved to be level at half-time and a they took the initiative early in the second half; a cross by Coke was a fraction too high for an unmarked Best.
A double substitution by Uwe Rosler in only the 54th minute, which saw the arrivals of forwards Nick Powell and Callum McManaman, represented a compliment to Wednesday’s efforts.
Maguire and Prutton took over from Maghoma and Oshilaja in the 62nd minute.
Wigan enjoyed a decent amount of possession in this half without managing to hurt this tenacious Wednesday side - but they should have done in the 79th minute.
The home team switched play to the right side of the box, where McManaman was unmarked. With time to try to pick his spot, the winger fired hard and low past the far post.
The Owls were not so lucky in late pressure by the home side.
Lavery helping out in the box, was penalised for a challenge when there seemed to be minimal, if any, contact with right-back James Perch, who seemed to go down theatrically. Haines gave a penalty and although Martinez went the right way, to his right, midfielder Jordi Gomez hit the top corner.
Meanwhile, Gary Madine notched the first goal of his comeback as the Owls Under-21s beat Hartlepool 6-1 at Middlewood. The other scorers were Manny Dieseruvwe 2, Rhys McCabe, Rafa Floro and Jack Stobbs, and Joe Wildsmith saved a penalty.
Goal: Gomez 88 (pen).
WIGAN: Al Habsi 6, Perch 7, Barnett 7, Boyce 7, Beausejour 7, Gomez 8, McArthur 6 (Powell 54), Tunnicliffe 7, McClean 6 (Fortune 72), Maynard 6, Waghorn 6 (McManaman 54, 6). Unused subs: Carson, Crainey, McEachran, Ramis.
OWLS: Martinez 7, Buxton 7, Onyewu 7, Loovens 7, Helan 7, Palmer 7, Coke 6, Oshilaja 7 (Prutton 62, 6), Lavery 6, Maghoma 7 (Maguire 62, 6), Best 6 (Nuhiu 75). Unused subs: Davies, J Johnson, Afobe, Llera.
Referee: Andy Haines (Tyne And Wear).
Attendance: 15,039 (1,924 away).