Emile Heskey, back after suspension, was desperately unlucky not to fire Wigan in front, but there were vital contributions from Latics keeper Chris Kirkland and Arsenal's Jens Lehmann before Adebayor got the winner, racing onto a great ball from Cesc Fabregas.
Carried off at Middlesbrough and forced to spend Saturday night in hospital, Kirkland was given a vote of confidence and named in the starting line-up.
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Wigan had Paul Scharner missing after picking up a one-match ban and that meant a chance for Dutch star Denny Landzaat.
Defensive strongman Kolo Toure returned for the Gunners, while Theo Walcott, Freddie Ljungberg and Julio Baptista were included in the starting line-up.
Much to Wigan's relief, Thierry Henry - who banged in five goals against the Latics last season - was again among the absentees with both sides still having major injury problems.
Arsenal produced the first threat of the game with Mathieu Flamini firing over from the edge of the area. But they survived a couple of scares as Henri Camara's tricky footwork and speed caused problems for their defence.
He hammered in one cross aimed at Heskey which was turned away for a corner, and then Camara failed to get a clear contact in a goalmouth scramble after Arsenal had initially failed to clear Kevin Kilbane's deflected shot.
Adebayor tried his luck after Gael Clichy set up the strike but it flew well wide of Kirkland's left post without troubling the keeper.
Camara seized the chance for a snap-shot but it swerved wide of the target and Emmanuel Eboue was fortunate not to be punished for a sloppy pass which presented Heskey with the opportunity to shoot.
Lee McCulloch's control in the area let him down after Wigan had engineered another opening and it was goalless at the break with neither keeper called on to make a save in the opening 45 minutes.
But all that changed in a much livelier second half.
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The Gunners then struck on the counter with Kirkland forced to beat out the shot from Baptista and he was involved in the action again, saving bravely from Adebayor.
There was another let-off for Wigan when Walcott got free on the right but he opted not to shoot and his pass inside failed to find Adebayor.
Lehmann kept out another effort from Josip Skoko, and Brazilian Baptista was just inches away from giving Arsenal the lead with a free-kick.
Lehmann did it again, beating out a fierce effort from Skoko, and the follow-up from Camara was blocked.
In a frantic closing spell, Kirkland saved from Ljungberg and showed his bravery to go down at the feet of Adebayor while, at the other end, Camara blazed over the bar.
Then, with time running out, Adebayor raced onto a great Fabregas pass, and hit his shot under Kirkland to break Wigan hearts.