Arsene Wenger's side's victory comes at a price as both Fabregas and Walcott leave the game injured
Arsenal got out of the traps quickest and could have been one up within the first minute when Jack Wilshere ran at the Stoke defence, before laying the ball off to Cesc Fabregas who played a wonderful reverse pass for Theo Walcott, but the his effort cracked the inside of the post and rebounded safely to Asmir Begovic.
Walcott was through again moments later after Nicklas Bendtner slid a neat pass between the Stoke defence, but Robert Huth and Danny Pugh combined to deny the England man getting a clear strike on goal.
The Gunners' early pressure paid off as they took the lead in the eighth minute through Squillaci, who headed home after Wilshere’s corner was knocked back into the six yard-box by Bendtner, whose harassing of Huth forced a corner for the home side.
Arsenal were then forced to substitute Fabregas, with the Spaniard appearing to tweak a muscle, and was duly replaced by Andrei Arshavin with Arsene Wenger refusing to take any chances ahead of the League Cup final, and trip to Barcelona on the horizon.
The Potters finally got into the game when John Carew forced a brilliant save from Wojciech Szczesny, who parried the Norwegian’s powerful half-volley away from goal after the striker latched onto Jon Walters’ knockdown.
Minutes before the break the Gunners had the chance to double their lead with a free-kick just outside the area however Samir Nasri wasted the opportunity by blasting wide of Begovic’s goal.
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Stoke came out in the second half the livelier and could have got back into the game through Ryan Shawcross, whose goalbound header was deflected wide after he escaped his marker to latch onto Jermaine Pennant’s cross.
The visitors threatened again minutes later from a trademark Rory Delap throw-in which Huth could have done better with as he rose above the Arsenal defence, but his header sailed harmlessly over the bar. Nonetheless, the Potters were coming more and more into the game.
Arsenal tried to respond to the Potters' pressure and Wilshere had a decent effort at goal as he tested the handling ability of Begovic but the Bosnian was equal to it.
Minutes later Walcott missed a glorious chance to make the Gunners lead more comfortable as he sliced his shot wide after great work from Arshavin who created the opening.
The home side suffered another injury blow in the 70th minute when Walcott fell to the ground after a challenge from Dean Whitehead. The England winger had to be stretchered off after appearing to turn his ankle in the fall.
This did not deter the Gunners from attacking Stoke however, as they looked to kill the game off, and Bendtner could have put the game beyond doubt had he kept his header down from Wilshere’s corner after beating Begovic to the ball.
Former Arsenal man Pennant then struck a rasping free-kick as the visitors went close to getting an equaliser for Potters in the last minute of normal time, but saw his effort creep just wide of the post, but Stoke were continuing to threaten the home side’s net.
The visitors continued to pile the pressure on the hosts but Wenger’s side defended resolutely, and held out to claim a vital three points to close the gap on leaders Manchester United.