Wednesday lost another player as well as a match last night as their unbeaten run came to a sobering end in the 12th game of their splendid revival.
The Owls, already hit by injuries, saw Jose Semedo carried off after a worrying six-minute hold-up in the second half when they were trailing to a double by striker Nicky Maynard.
At that point Wednesday were struggling to overcome the FA Cup holders, who showed some of their Premier League pedigree and for the second time this season were strong, classy and one of the best visiting teams seen at Hillsborough. But the contest see-sawed in a 10-minute spell in the first half.
Strike partners Atdhe Nuhiu and Benik Afobe had opportunities to engineer goals; then Maynard gave a lesson in finishing to put Wigan ahead and poached the second goal from a corner.
Wednesday applied pressure in the second half but the Latics defended solidly and snatched a third goal on the break through Marc-Antoine Fortune in the second of eight added minutes, the ball coming out to the sub after a Chris Kirkland save denied Maynard a hat-trick.
Stuart Gray made two changes to the side that started at Reading. Adedeji Olishaja made his debut and Atdhe Nuhiu was recalled, with Rhys McCabe and Jeremy Helan dropping to the bench, and Semedo switching back to midfield from centre-half.
Oshilaja, able to play after his international clearance arrived at last, settled in quickly with some crisp touches and a firm tackle.
But the on-loan Cardiff youngster, whose only previous league experience was in League Two in a loan spell at Newport, soon saw the quality that the Championship can boast.
He was one of four players powerless to halt a weaving run from James McClean before the left winger finished feebly.
If that would have been a great goal, one by Miguel Llera would have been even better.
Seeing Ali Al Habsi well off his line, the centre-half went for goal from a free-kick just inside his own half. The ball dropped wide but the keeper seemed none too comfortable as he had to make ground back towards his own goal.
A goal then in the ninth minute would have given Wednesday a firm, early platform like the one they constructed at Reading.
But Wigan, playing towards the Leppings Lane end where their fans were few, showed the same sort of ability that was on display in the abandoned game between the clubs in December.
They played Maynard on his own up front but had players breaking forward.
Wednesday, however, had the best chance of the first half hour.
Nuhiu won the ball on the right of the box and Benik Afobe was waiting unmarked in the middle. But Nuhiu sent a tame, left-foot shot straight at the keeper - and it was another failure by the striker who twice chose to shoot near the end of the Reading game when teammates were better placed.
Afobe was next to mess up, two minutes later. He showed his pace and strength like he did last Saturday when he won a penalty by getting in behind a defender.
This time he could have got in an early shot but tried to beat a second opponent in the box, slipped and knocked the ball towards Al Habsi.
Those errors seemed even more costly when, a minute later, Martyn Waghorm pierced the Wednesday defence with a pass and Maynard fired home, in the 31st minute.
The Owls found themselves under pressure and fell two down seven minutes later.
Waghorn whipped in a wickedly inswinging low corner from the right with his left foot and it appeared to fly straight in, but there was also a suggestion that Maynard got a slight touch in the middle.
The scale of Wednesday’s task now was illustrated by Wigan’s pulling of nine men behind the ball to protect their lead when the Owls attacked.
Stuart Gray made a double substitution in the 55th minute in an attempt to find the missing penetration.
He took off Jacques Maghoma and Afobe, sent on Michail Antonio to the right flank and Jeremy Helan to the left, and pushed Chris Maguire up front.
With virtually his first touch, Helan hit a splendid long-range effort and Al Habsi touched it over the bar.
A minute later came a chance: A left-wing cross by Semedo and a downward header by Miguel LLera which lacked power and was saved at the foot of a post.
That was Semedo’s final contribution. In the 58th minute he stretched into a challenge, went down and then raised his arm - usually a signal that it is something serious.
There was a six- minute hold-up while he received attention and was carried off.
Caolan Lavery replaced him. Helan switched to central midfield, Antonio took his place on the left and Maguire went back to the right .
Lavery headed a chance over the bar in the 75th minute, Maguire had a brilliant 30-yard shot saved and Al Habsi denied Antonio, as the Owls threw everything at the opposition.
But Wigan defended well under pressure and deserved the points, even if 3-0 did flatter them a little..
Meanwhile, Reading centre-half Alex Pearce has succeeded in a appeal against his sending-off in the match against the Owls last Saturday. The FA announced the decision yesterday.
Pearce was dismissed for a foul on Afobe in the ninth minute, which resulted in Maguire scoring the penalty that sent the Owls on their way to a 2-0 win.
The referee judged that Pearce had denied Afobe a goalscoring opportunity.
Reading manager Nigel Adkins believed that this was wrong and claimed that defender Kaspars Gorkss was running in to cover behind Pearce.
Goals: Maynard 31, 38; Fortune 90+2 (Wigan).
Owls: Kirkland 7, Palmer 7, Llera, Oshilaja 7, Mattock 7, Maguire 6, Semedo 7 (Lavery 64, 6), Lee 7, Maghoma 6 (Antonio 55, 7), Nuhiu 6, Afobe 6 (Helan 55, 7). Subs not used: Martinez, McCabe, Corry, McPhail.
Latics: Al Habsi 7, Perch 7, Boyce 7, Barnett 7, Beausejour 7, Waghorn 7, McCann 6, Watson 7, McArthur 7, McClean 6 (Fortune 51, 6), Maynard 8. Subs not used: Nicholls, Crainey, Gomez, McManaman, Espinoza, Kieman.
Referee: David Webb (Lancashire).