Ricardo Fuller and Seyi Olofinjana both scored after long throw-ins by Rory Delap as Arsenal capitulated and also had Robin van Persie sent off.
Delap sent a throw to the far post and Fuller glanced in for the opener.
Delap, himself, then looped in a header that Gael Clichy cleared off the line before Olofinjana chested in Stoke's second from another Delap throw-in.
Van Persie saw red for shoving Thomas Sorensen before Clichy pulled a goal back with a deflected shot.
The defeat is another serious blow to Arsenal's title aspirations, while Stoke will be delighted with three points that take them a little further away from the drop zone.
There was nothing pretty - or surprising - in the way Stoke went about their business, but it proved effective.
An Arsenal side selected to cope with their opponents' physical presence struggled to handle Stoke strike pair Fuller and Mamady Sidibe.
And a combination of Delap's speciality throw-in and Fuller's strength cost Arsenal dear as the pair fashioned Stoke's opener.
Kolo Toure was dominated by Fuller, whose deft touch to Delap's delivery sent the ball past keeper Manuel Almunia.
Arsenal, lacking the guile and pace of Robin van Persie and Theo Walcott - both on the bench - looked disjointed and bewildered.
606: DEBATEAnd it could have been worse for the Gunners had Delap managed to get a little more power on a goalbound header that Clichy cleared.
A tame Emmanuel Adebayor shot that Sorensen comfortably gathered was the best Arsenal could muster.
The Gunners brought on Walcott on 57 minutes in the hope of adding some thrust to their play.
But with Cesc Fabregas a shadow of himself, one wondered where the England youngster's supply line would come from.
Instead it was the hosts who almost scored when another Delap throw caused mayhem and Salif Diao's volley from the edge of the area was superbly saved by Almunia.
It was a warning that Arsenal failed to heed, and from Delap's next throw-in, Ryan Shawcross nodded on and Olofinjana scrambled the ball over the line, nudging it forwards twice with his chest.
Worse was to come on a miserable day for the visitors when Van Persie, on the pitch for only 12 minutes, was dismissed after needlessly barging into Sorensen.
And boss Arsene Wenger could also be without three other first-teamers in the coming weeks because of injuries. Walcott was stretchered off with a shoulder problem, while Adebayor and Bacary Sagna also left the field with knocks.
Clichy's late effort from the edge of the box went in with the help of a couple of deflections.
But there was to be no great escape for Arsenal, and they would not have deserved one.
Stoke: Sorensen, Griffin, Abdoulaye Faye, Shawcross, Higginbotham, Amdy Faye, Olofinjana, Diao (Whelan 78), Delap, Fuller (Cresswell 86), Sidibe (Kitson 90).
Subs Not Used: Simonsen, Soares, Wilkinson, Sonko.
Booked: Higginbotham, Sidibe, Delap, Cresswell.
Goals: Fuller 11, Olofinjana 73.
Arsenal: Almunia, Sagna (Walcott 57), Toure, Silvestre, Clichy, Denilson (Van Persie 65), Fabregas, Song Billong, Diaby, Adebayor (Vela 72), Bendtner.
Subs Not Used: Fabianski, Nasri, Ramsey, Djourou.
Sent Off: Van Persie (76).
Booked: Adebayor, Fabregas.
Goals: Clichy 90.
Att: 26,704
Ref: Rob Styles (Hampshire).
BBC Sport Player Rater man of the match: Stoke's Rory Delap 7.65 (on 90 minutes).
Please note that you can still give the players marks out of 10 on BBC Sport's Player Rater after the match has finished.
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