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The Gunners began brightly with Theo Walcott looking lively on the right flank.
Thierry Henry and Julio Baptista looked threatening and the latter was just inches away from getting on the end of a through ball from Henry after just four minutes.
Tomas Rosicky on the left flank was also looking dangerous with the Czech international forcing Chris Kirkland into a fine save on ten minutes and then hitting a fiercely struck effort just wide of the right post two minutes later.
Just before that, Jens Lehmann was forced to parry a 25-yard thunderous effort from Denny Landzaat - but better was to come from the midfielder.
The Gunners should really have taken the lead just before the quarter hour when Henry was free inside the six-yard area all alone. The normally reliable Gunners captain somehow blazed his left-footed effort high over the bar.
It was Wigan, however, who opened the scoring through Landzaat, whose 25-yard 35th minute shot winged its way high into the top left corner beyond Lehmann's despairing dive.
The visitors should have doubled their lead on 40 minutes when a ball over the top of the Arsenal defence fell on to the outstretched boot of Julius Aghahowa, but the Nigerian sliced his shot high and wide from five yards.
Emile Heskey thought he had made it 2-0 right on half-time when the Wigan striker ran on to a perfectly weighted ball from Ryan Taylor.
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Within seconds the ball was at the other end with Henry rising high to meet a Gael Clichy cross from the left, but his downward header bounced just wide of the left post.
The Gunners began the second half attacking the West Stand where 70 per cent of goals at the Emirates have been scored.
Heskey again went close to putting a dent in that statistic on 50 minutes when he latched on to a ball over the top. He accelerated into the right side of the Arsenal are but his effort was wide of the target.
A minute before that, the Wigan striker had put an arm across the face of Johan Djourou which signalled the end of the youngster's game and forced Arsene Wenger to gamble perhaps a little earlier than he had wanted.
The Arsenal boss sent on Emmanuel Adebayor with Gilberto stepping back into central defence.
Wigan didn't detract from their tactics and kept venturing forward whenever they could break.
Adebayor had a goal ruled out for offside on 72 minutes and Wigan's resolute defending looked as it may earn the visitors an unlikely three points.
But a Fitz Hall own goal on 81 minutes put paid to those hopes. The move began when Cesc Fabregas found Adebayor, who in turn slipped a ball into the path of an offside looking Mathieu Flamini.
The Frenchman delivered a cross towards Henry but it was diverted into his own net by Hall just before the Frenchman's outstretched boot reached the ball.
Wigan Manager Paul Jewell was still seething as his side were denied what looked like a penalty when Flamini hauled down Heskey.
The Gunners took advantage of Wigan's disarray and made it 2-1on 85 minutes when Adebayor found Baptista on the right wing.
The Brazilian then drilled a cross towards goal that was headed home from close range by Rosicky to claim all three points.