The Latics, who beat champions-elect Manchester United at home on Wednesday, began in a blaze of glory by scoring twice inside the opening ten minutes before conceding. It then appeared as though the Gunners would fight back at least for a draw but Roberto Martinez's side were brilliant in all aspects and managed to hold out for a win which sees them move five points clear of the relegation zone.
Wigan opened the scoring in just the seventh minute when they worked a fast break from an Arsenal corner with Jordi Gomez finding Franco di Santo whose initial attempt from the edge of the box deflected up off the advancing Wojciech Szczesny and back into his path for the Argentine to poke home.
The goal was against the run of play but if that had taken the Gunners by surprise, they were shellshocked about a minute later when Victor Moses made a dazzling run down the left before cutting back from the byline with the ball rolling through to Gomez whose toe-poked effort was saved by Szczesny before it fell back to the Spaniard to slot into the back of the net.
Arsenal lifted the tempo after that second goal and got one back in emphatic style when Tomas Rosicky found space on the right before floating a pinpoint ball into the area for Thomas Vermaelen to power a header home, raising the spirits of the home crowd.
Earlier, Wigan keeper Ali Al Habsi had kept his side in it when he did brilliantly to deny Yossi Benayoun headers in the sixth and 16th minutes, both world class stops, before thwarting Robin van Persie's long range effort as the Gunners applied pressure.
Wigan had chances of their own with the electric Moses seeing his angled effort early in the second half saved by Szczesny before the Latics reverted to a more defensive approach which frustrated the North Londoners to no end.
Arsene Wenger's men huffed and puffed for the remainder of the match but a disciplined Wigan outfit came shining through to follow up Wednesday's win over league leaders United to make it four victories from their past five outings.
For Arsenal, it was a missed opportunity to go eight points clear of Tottenham and Newcastle United as they dropped points to a team in the bottom five for the second time in four games after the QPR loss at the end of March.
Emirates Stadium, London - 60,060