Early goals from Franco Di Santo and Jordi Gomez prevented Arsenal from moving further clear of the chasing pack in the race for third place as the Latics won 2-1 at the Emirates.
Thomas Vermaelen responded soon after for the Gunners but they could not find a leveller as Wigan's defence dealt with everything Arsenal had to offer.
Despite the fact the home side started the brighter it was Wigan who took a shock lead when Gomez fed Di Santo who had his first shot blocked by Wojciech Szczesny but bundled home the rebound.
Within 94 seconds the Emirates was in utter silence, Wigan broke again and this time Victor Moses' superb trickery allowed him to beat Bacary Sagna and after Szczesny spilled James McArthur's strike Gomez tapped home to make it 0-2.
Arsenal's reponse was immediate, Yossi Benayoun almost halfing the deficit with a brilliant header matched by Ali Al-Habsi's excellent stop.
The unfortunate Mikel Arteta was subbed for Aaron Ramsey through injury, one that hopefully is not serious, and Arsenal looked better when the Welshman entered the field.
After 20 minutes Arsene Wenger's side were right back in it, Tomas Rosicky's cross picked out Vermaelen who headed past Al-Habsi to awaken the Emirates crowd.
At that moment you could have been forgiven for expecting an Arsenal onslaught to turn into a victory, but the Latics have been hard to beat of late and so the case proved tonight.
Rosicky blazed over after a neat one-two with Van Persie and Andre Santos almost missed a good chance.
Wigan almost restored their two goal lead when Gomez had a go from range but his shot went wide.
The second half began well for Arsenal, Santos twice coming close inside the opening minutes.
But as the game grew on as did the home fans frustration and the away side's belief.
Alex Oxlade-Chamberlain breathed fresh life into the Arsenal side but Wigan stuck nearly everyone behind the ball for the last half hour and the hosts ran out of ideas.
The Gunners did not create any really clear cut chances in the second period as the Latics held out for a memorable win, the final whistle was met by boos from the home crowd, who were understandbly frustrated, but Wigan deserve credit.
Arsenal were not that bad, and they will play worse and win matches, Wigan just did what they had to do, and the did it well.