On-loan Mido gave the Latics the lead and Ben Watson was denied a second by the woodwork after Arsenal's Kieran Gibbs had been fortunate not to be sent off when he brought down Luis Antonio Valencia in the first half.
Egypt star Mido was also unlucky to have a header cleared off the line after the break before the Gunners hit back with a killer double.
Theo Walcott got the equaliser and Mikael Silvestre hammered in the second as Arsenal stretched their unbeaten league run to 18 games with Andrey Arshavin and Alexandre Song adding to Wigan's agony with
late strikes.
The Gunners were below strength with Manuel Almunia, Gael Clichy,Abou Diaby and William Gallas among the absentees and for Wigan Hugo Rodallega replaced the injured Charles N'Zogbia, the only change from last week.
The Latics deservedly took the lead when Mido's free-kick came off the wall and went for a corner. Watson floated it into the box, it was headed back in by Paul Scharner and Mido struck from six yards.
It took a touch off Bacary Sagna and, although keeper Lukasz Fabianski got a hand to it, he could not keep it out.
Wigan - and their fans - were furious when Valencia was brought down by Gibbs as he raced in on goal.
It looked like a red card offence but ref Alan Wiley opted for yellow and, from the free-kick, Watson's shot hit the post.
Rodallega hammered a free-kick over the bar and Mido was desperately unlucky not to get his second of the game.
He went in bravely as the keeper raced out and still got in the header but Gibbs got back to stop it crossing the line.
Mido, who needed treatment for cuts to the mouth, had to be replaced by Olivier Kapo.
Chris Kirkland had not had a save to make before Arsenal grabbed the equaliser on the hour after Arshavin managed to get the ball to Walcott and the young England star made no mistake from ten yards.
The unmarked Silvestre then thumped in the second and Arshavin hit the post with Robin van Persie ruled to be just offside when he fired the rebound past Kirkland.
The Latics kept plugging away with Watson testing Fabianski with a free-kick, and Scharner shooting wide, but Arsenal finished in style with those two late goals by Arshavin and Song.