FootyMAD Match Report direct from the press box
Wayne Thomas fired the Potters ahead seconds before the interval, but second-half strikes from Jose Antonio Reyes and Robin van Persie ensured a shock was averted.
Stoke started strongly and had the first real effort on target after ten minutes when the powerful Ade Akinbiyi opened up an opportunity for himself on the right side of the Arsenal penalty area, but his fiercely struck shot was well saved by Jens Lehmann.
The visitors opted to defend in numbers and attack the champions on the break, and the tactic served to largely restrict Arsenal to a string of long-range efforts that were comfortably dealt with by the impressive Steve Simonsen.
The home side's first real chance came after 26 minutes when van Persie had an effort from the outside of the area easily saved by the visitors' keeper.
Simonsen was on hand again five minutes later when he saved more spectacularly from Jermaine Pennant, who latched onto a pass from Robert Pires before unleashing a shot that was palmed to safety the City custodian.
Pires headed just over from a Pennant cross minutes later but then Stoke went back on the attack. Akinbiyi, who proved to be a thorn in the side of Arsenal centre-back Kolo Toure, won the battle on the left flank and cut inside before crossing for the waiting Chris Greenacre, but his shot was wide of Lehmann's goal.
The Championship side thought they had a goal a minute later when a ball into Arsenal's penalty area was allowed to bounce by Philippe Senderos and Akinbiyi lifted the ball over Lehmann and into the Arsenal net - but the effort was ruled out for an innocuous looking push by the Potters front man.
The visitors were not too disheartened and continued to press forward, grabbing their reward a minute into injury time at the end of the first half.
A cross came over from Greenacre and Akinbiyi rose highest to head the ball towards goal. Lehmann made a point-blank save but could only parry the ball as far as Thomas, who lifted his shot into the roof of the net from two yards out to ensure Stoke went into the interval a goal up.
Arsene Wenger clearly had some inspirational words for his players at half-time and they came out of the tunnel with a renewed sense of urgency.
Van Persie went close just three minutes after the restart when supplied by a delightful Cesc Fabregas ball into the left side of the area but his first-time shot was well saved by Simonsen.
The Gunners were back on level terms shortly after 50 minutes when Toure managed to get to the byline and deliver a cross which was only cleared as far as the feet of Reyes, who fired a left-foot shot powerfully into the net.
Despite the setback City continued to pose a threat and Greenacre shot just wide after 55 minutes before seeing Gael Clichy clear another effort off the line four minutes later.
From then on the Gunners took control and Reyes, Pires and van Persie all went close.
Akinbiyi was unlucky after 67 minutes when he lobbed the Arsenal keeper, who was relieved to see the dipping effort bounce off the crossbar to safety.
Arsenal's victory was sealed in the 70th minute when Pennant crossed for van Persie to fire a volley into the back of the net, giving Simonsen no chance.
The Premiership side continued to push forward and another great Simonsen save in injury-time denied Pennant and kept the score at 2-1.