Thomas Vermaelen had been controversially sent off at the end of the first half, but the Gunners continued to outplay their guests from East London and a first-half goal from Denilson and a late penalty from Cesc Fabregas saw Arsenal move above Manchester United and Chelsea.
The Gunners stormed to an early need just over four minutes into the game with a strike from just inside the area from Denilson.
The midfielder first received the ball in a central position on the edge of the area and looked to have let the opportunity pass, but some quick feet saw him finding Nicklas Bendtner, who in turn returned the ball for the Brazilian to drill a low shot past Robert Green into the right side of the net.
West Ham did well following the goal to take the sting out the game and keep the Gunners from really further testing Green for much of the remainder of the first half. Their tackling was strong, occasionally straying into the realms of excessive, measured by the fact that Arsene Wenger rarely took his seat.
Alessandro Diamanti was a bit of a thorn in Arsenal's side, his unpredictability and invention being at the heart of most of the visitors' best moves.
Manuel Almunia was rarely tested and the first shot on target of note came in the 41st minute from Junior Stanislas and even that was easily claimed by the Spaniard.
The Irons were handed a massive opportunity with a decidedly questionable penalty and sending off of Vermaelen. The Belgium international was adjudged by referee Martin Atkinson and his assistant Phil Sharp to a have pushed over Guillermo Franco.
Diamanti stepped up to despatch the spot-kick, but Almunia guessed right and dived to his left to parry the well-struck effort.
While undoubtedly pleased by the save, Wenger was furious and waited at pitchside at half-time to remonstrate with the referee, giving him both barrels as he followed him down the tunnel.
The second half began with Alex Song moving back into defence, with Denislon sitting just in front of the back four as the main anchor.
In response, Gianfranco Zola pushed his attackers further up the pitch, clearly now keener to take advantage of a depleted Arsenal.
Almunia had to be at is sharpest in the 52nd minute when he reacted quickly to catch Fabio Daprela's deflected shot before it crept in at his near post.
Despite being down to ten men and the introduction of Carlton Cole and soon after Benni McCarthy, the Gunners continued to control the game and pose the bigger threat.
Sol Campbell and Andrey Arshavin forced decent saves out of Green. Cole's nimble turn and shot in the 77th minute beat Almunia, but struck the outside of the right post, to the relief of the home fans.
Late on Atkinson gave his second penalty of the game, this time to Arsenal and this time it was converted. Former Gunner Matthew Upson, already on a yellow card, handled the ball in the area.
Fabregas sent Green the wrong way and the Emirates erupted as the ball nestled in the bottom left corner of the net with seven minutes of regular time to play.