Thierry Henry scored two of the Gunners' goals which now places them just three points behind Premiership leaders Liverpool.
Villa's Merson and Dion Dublin were a force to be reckoned with as Dublin headed on a pass to Merson who neatly sent the ball over Arsenal keeper Stuart Talyor.
In the 34th minute Stone picked up a poor clearance to make it 2-0.
With the London side trailing 2-0 at the close of the first half after a great counter-attack from Villa, it was a tense 15-minute break.
But the Gunners came through firing on all cylinders, with substitute Wiltord pulling one back with a volleyed goal before watching Henry fire in his two goals.
Other matches:
Blackburn 1-2 Leeds United
Leeds got a lucky and vital three points against Blackburn. Two Harry Kewell goals in the second-half assured them of the points.
But there was fierce attacking late in the game by Blackburn, when Henning Berg managed to score in the 82nd minute.
Ipswich Town 0-1 Newcastle United
The Magpies were in full flight against Ipswich, grabbing three points thanks to a Nolberto Solano 20th minute strike.
It wasn't a good game for Ipswich and they were never a danger to Newcastle keeper Shay Given.
Sunderland 0-0 Chelsea
Sunderland failed to make any head-way after several attempts at goal against Chelsea.
But keeper Carlo Cudicini was on top form, blocking a penalty form Kevin Phillips as well as shots on target.
