Franco Di Santo fired the Latics - who last week beat leaders Manchester United - ahead on the break after seven minutes, before Jordi Gomez doubled their lead inside 90 seconds.
Thomas Vermaelen reduced the deficit with a bullet header on 21 minutes, but the second-half onslaught from the shell-shocked Gunners never came as the Latics moved five points clear of the relegation zone.
The Latics had brought a small following of only some 200, who had perhaps travelled more in hope than genuine expectation.
Newcastle are five points behind the Gunners but have a game in hand.
ARSENAL
Arsenal v Chelsea
Stoke City v Arsenal
Arsenal v Norwich City
West Bromwich Albion v Arsenal
NEWCASTLE UNITED
Newcastle United v Stoke City
Wigan Athletic v Newcastle United
Chelsea v Newcastle United
Newcastle United v Manchester City
Everton v Newcastle United
Wigan manager Roberto Martinez: "I'm so so satisfied because that wasn't an accident.
"In eight days, to have to play Chelsea, Manchester United and Arsenal is such a big task, but today in the manner that we coped physically and tactically, everyone at Wigan Athletic should be very proud.
"In the second half, to have that mentality of know-how in such a young group, to understand what's needed in different phases, we coped with an outstanding footballing side.
"It was a well-deserved three points, and to say that speaks volumes of the performance of the players."