Arsenal claimed third place in the table after narrowly beating Wigan.
Adebayor scored his fourth league goal this season
The visitors were frequently troubled by Henri Camara, whose superb pass released Emile Heskey, who badly missed with his shot early in the second half.
That sparked an Arsenal reaction, with Julio Baptista's shot saved by Wigan keeper Chris Kirkland, while Emmanuel Adebayor went close several times.
And with three minutes left, substitute Cesc Fabregas' pass released Adebayor, who poked the ball past Kirkland.
Arsenal manager Arsene Wenger opted to leave Fabregas, along with Alexander Hleb and Robin van Persie on the bench, three players who had played so well in the 1-1 draw with Chelsea on Sunday.
The absence of Fabregas was particularly felt with Arsenal's attacking movements lacking imagination in the first half, a period of play where Wigan were on top.
The last time Paul Jewell's side played at home they were losing 4-0 at half-time to Liverpool, but this time the Latics were altogether more cohesive in attack and defence.
Wigan's best player was Camara, who gave Arsenal left-back Gael Clichy all sorts of problems with his speed and footwork from the moment he delivered an early cross for Heskey.
Camara had Wigan's best first-half chance, but under pressure from Johan Djourou the Senegal international's shot went wide.
The second half was an altogether more absorbing affair.
Camara played a wonderful reverse pass to leave Heskey with just Jens Lehmann to beat, but the Wigan striker embarrassingly miscued.
That prompted Arsenal to retaliate, Adebayor releasing Baptista, whose shot was well saved by Kirkland.
The Wigan goalkeeper saved his side for a second time when he came out quickly to deny Adebayor, who had been sent clear by Gilberto.
Soon afterwards Theo Walcott overhit his cross and Adebayor was unable to connect with the ball as Arsenal carved apart Wigan for a third time.
Wenger introduced Van Persie and Fabregas to try and press home Arsenal's advantage, but as those two players adjusted to the game's rhythm, Wigan came close to taking the lead.
Josip Skoko's shot was only partially saved by Lehmann, requiring Kolo Toure to throw himself at the ball to block Camara's close-range effort from the rebound.
With the game seemingly heading for a draw Fabregas sent a curving pass over the Wigan defence to the feet of Adebayor and the Togo striker made no mistake slipping past Kirkland.
Wigan manager Paul Jewell:
"I thought we were terrific. They had a few chances in the second half - but I thought we played really well.
"People will say it was a great pass for the goal, but we lost concentration and switched off for a second.
"We paid the price, losing the game - which I didn't think we deserved."
Arsenal manager Arsene Wenger:
"It was a difficult game - Wigan were up for it. It could have gone for them but it went for us.
"We created chances but they had one or two and we needed to be strong to claim the three points.
"Sometimes when you play every three days you have problems getting into the game but it gets better."
Wigan: Kirkland, Wright, Boyce, Hall, Baines, McCulloch, Landzaat, Skoko, Kilbane, Camara, Heskey (Johansson 67).
Subs Not Used: Pollitt, Jackson, Cotterill, Todorov.
Arsenal: Lehmann, Eboue, Djourou, Toure, Clichy, Walcott (Hoyte 89), Flamini (Fabregas 74), Julio Baptista (Van Persie 75), Silva, Ljungberg, Adebayor.
Subs Not Used: Almunia, Hleb.
Goals: Adebayor 88.
Ref: R Styles (Hampshire).