Khalid Boulahrouz was sent off in the first half of today's game for bringing down Julio Baptista with Gilberto Silva converting the penalty.
Michael Essien equalised with a header in the second half but it was not enough to give United their ninth Premiership crown.
Ashley Cole missed the game because of an ankle injury while Didier Drogba and Claude Makelele were left out of the starting line-up.
Youngster Denilson started for the Gunners in midfield ahead of Alexander Hleb in the absence of Tomas Rosicky.
The opening half was subdued with both sides failing to find any kind of rhythm.
Frank Lampard came close to scoring on 33 minutes when the midfielder just failed to get a touch on Joe Cole's ball across the six-yard box.
The first clear-cut chance came on 37 minutes when some slick passing from the hosts ended with Emmanuel Adebayor scuffing his shot from the edge of the box straight at Petr Cech.
The turning point of the match occurred on 42 minutes when Khalid Boulahrouz brought down Julio Baptista after some hesitant defending.
Referee Alan Wiley pointed to the spot and sent-off the Dutchman for being the last defender.
Gilberto Silva stepped up and sent Cech the wrong way after slotting home into the bottom right corner to open the scoring.
Arsenal continued to dazzle with their passing in the second half with Adebayor just failing to pull the trigger from Cesc Fabregas' back-heel.
The north London side were temporarily down to ten men on 59 minutes after Denilson was replaced by Hleb after a feisty challenge from Paulo Ferreira.
Wenger's side continued to bombard the Blues area with shots with only a last-gasp block from John Terry denying Hleb on 64 minutes.
William Gallas missed a golden chance to sink his former club on 66 minutes after heading over the bar from close range following a corner.
Against the run of play, the Blues pulled level after Shaun Wright-Phillips' cross was glanced in by Essien to make it 1-1.
Cole had the ball in the net ten minutes later but the flag had already gone up for offside.
Eighteen-year-old Scott Sinclair came on in the closing stages in place of Wright-Phillips as the Blues tried to keep the title race alive.
Terry was playing as a centre-forward for the final ten minutes and helped the Blues win a corner which led to Essien firing over from close range.
In a dramatic finale, Cech denied Hleb with a stunning save followed by Jens Lehmann tipping over Salomon Kalou's side-footed strike.
In stoppage time, Emmanuel Eboue's piledriver struck the woodwork before the full whistle blew to signal the end of Chelsea's reign as Premiership champions.
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