Jon Walters' second-half penalty was enough for Stoke to secure all three points over Arsenal at the Britannia Stadium.
Mark Hughes made one change to the side that lost to Manchester City a week ago, with Steven N’Zonzi coming in for Peter Odemwingie.
Jack Wilshere gave Stoke an early chance when he brought Charlie Adam down from behind but the resulting ball was poor and straight at Wojciech Szczesny.
The Gunners claimed the first corner of the match but Stoke’s defence were on the same page and managed to avoid any danger.
The hosts then broke following a second corner and Marko Arnautovic put in a deep cross but Walters headed just wide of the post.
Neither goalkeeper was tested inside the opening 25 minutes as both sides failed to take advantage of their chances in front of goal.
Olivier Giroud secured Arsenal’s first shot on target in the match but it was a tame header straight at Asmir Begovic.
Peter Crouch then fired wide from N’Zonzi’s cross. Glenn Whelan was having one of his best games for Stoke in a long time and he continued this as he hit a fine strike - but it was straight at the Arsenal keeper.
The visitors replied through Santi Cazorla who hit a low strike at Begovic, and the keeper had to react fast and claim it down low but he made it look easy.
Stoke seemed to have a lot more of the chances and the possession in the first half and continued this in the second as Geoff Cameron put in a cross and Crouch and Walters tried to break the deadlock, to no avail.
Arsenal found more space down the left hand side and tried to use this against Stoke as Giroud was ready to pounce but Marc Wilson cleared with an important header.
The breakthrough came in the 76th minute when Walters was then in the box and put in a strike that came off Laurent Koscielny’s hand. Referee Mike Jones pointed to the spot, Walters stepped up despite the fact that he missed his last one, and the Irishman put the ball beyond Szczesny to give Stoke the lead.
The Gunners tried to find the equaliser in the remaining few minutes, bringing on Yaya Sanogo, but his blazed a glorious effort over the bar in the closing stages.
The Potters secure their first win over Arsenal for two years, allowing them to climb up to 12th and further away from danger. They now face Norwich away next weekend, whilst Arsenal remain in second, ahead of Manchester City but just two points ahead.
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