Mauro Boselli scored his first Wigan goal as the Latics dumped boss Roberto Martinez's ex-club Swansea out of the Carling Cup to reach the last eight.
The £6m Argentine Boselli struck after the break, capitalising on a great charging run from Antolin Alcaraz.
Ben Watson wrapped up the win in injury time from the penalty spot after Charles N'Zogbia was hacked down.
Swansea had the ball in the net in the first half but Craig Beattie was adjudged to have been offside.
Most of the build-up surrounded the reunion between Martinez and Swansea on the first meeting since the former manager walked out on them 16 months ago for the Wigan job.
Interview: Wigan manager Roberto Martinez
He was roundly jeered by the 4,500 travelling Swans fans who have largely not forgiven him for leaving after previously saying he would have to be forced out.
But for Swansea, aside from targeting revenge, a place in the quarter-finals for the first time in their history was at stake.
Both sides made wholesale changes from their respective weekend matches and it was Swans boss Brendan Rodgers' side who were almost caught out in the opening exchanges.
A mix-up between goalkeeper Yves Makalambay and his defence on the edge of the box almost let Wigan in but they managed to scramble the ball to safety.
Mohamed Diame then charged towards the visitors' goal before launching a soft shot straight at Makalambay from 20 yards.
Craig Beattie found the net but had his goal disallowed
Swansea did have the ball in the net after nine minutes when Darren Pratley split the Wigan defence to put Cedric van der Gun clean through on goal.
Dutchman van der Gun could have shot, but instead laid off to Beattie to put the ball into an empty net, but the linesman's flag was up for offside.
Soon after Pratley was involved again, looping the ball over Alcaraz and into the box, but his touch was too heavy for his supporting strikers.
The Swans lost defender Albert Serran to injury so captain Garry Monk was called from the bench.
Both sides are known for their passing football and the excellent Victor Moses caused the visitors problems down the left with his pace.
But it was Jordi Gomez who could have put Wigan ahead, first with a left-footed shot, and later sending a 20-yard free kick into the wall after Alan Tate had tripped Diame.
The hosts' best chance fell on 30 minutes, though, when Watson slipped the ball through to Boselli but Makalamby came out feet first to deny him.
Roberto Martinez shakes hands with Brendan Rodgers
Wigan were ahead six minutes after the break after Alcaraz made a great run before slipping the ball superbly through to Boselli who rounded Makalambay.
It lifted the home side who put Swansea under pressure and ex-Estudiantes striker Boselli had the chance to double the lead moments later but headed just wide from a corner.
On the hour, the Swans wall blocked Watson's free kick from a Monk foul on Moses, and Makalambay did well to push away Figueroa's 30-yard rebound which came through a crowd of players.
Wigan were very much on top by now and Boselli caught Makalambay off his line, but the ex-Chelsea stopper reacted well to push it away.
Swans proud despite Wigan defeat
Martinez threw on N'Zogbia for Gomez while Rodgers replaced Beattie with Stephen Dobbie to add something to the Swansea attack.
It was Dobbie who cut in from the left and tried to pick out David Cotterill and the near post, but Ali Al Habsi was quickest.
Swansea pushed hard to force the game into extra time, but all hopes of gaining revenge on Martinez were ended in injury time when Andrea Orlandi tripped N'Zogbia and Watson converted the penalty into the bottom corner.
Wigan manager Roberto Martinez: "You can see Mauro is a really confident finisher. A goal scorer in football is expensive and the hardest thing to find.
"He is a real asset to our football club but we need to be patient and fair with him. He is coming from a different league, different environment, different culture.
"If you look at the way he has adapted, the work-rate, the way he took the goal, it is very pleasing.
"I am sure Wigan Athletic fans will see the best of him very soon."
Swansea manager Brendan Rogers: "We are obviously disappointed with the [Beattie] goal, if you see it again, you will see that it shouldn't have been disallowed.
"It was a wonderful break, the ball has been squared and at the point of contact Craig Beattie is onside. Obviously by the time he touches it he is in a forward motion and sweeping it in.
"I'm disappointed with the referee's or the linesman's positioning, but that is how it goes.
"I was very proud of the team. We have come to a Premier League club and shown we can hold our own, if not more than that.
"We created a number of chances. I'm obviously disappointed we couldn't take them but I am very proud of the team and the support we got was phenomenal."
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.