A 1-1 draw was the best they could achieve despite their dominance of possession and superiority of numbers.
Having claimed one major Premiership scalp already this season, Gareth Southgate's side were on course for a second having taken a shock lead 22 minutes into the game.
Their recent victory over Chelsea had no doubt boosted their confidence, but with goal hero against the Blues, Mark Viduka, on the bench, James Morrison stepped up.
The goal was a well-worked effort which began with a ball down the right flank from Andrew Davies into the path of Morrison.
The attacker then sped towards the Arsenal area, exchanging passes with Jason Euell, whose perfectly weighted ball split the Arsenal defence.
Morrison then showed coolness beyond his years to shoot across goal beyond the dive of Jens Lehmann to find the bottom left corner of the net.
The Gunners gave a debut to William Gallas and the French international was selected to operate at left-back.
Within three minutes of the kick-off he delivered a superb cross into the box for Robin van Persie that the Dutch striker failed to control to make the most of a good opportunity.
Arsenal were on the front foot from the opening whistle with Gilberto Silva heading just wide from a Thierry Henry corner on eight minutes.
Henry hit the target two minutes later but Mark Schwarzer was in place to make a fine save, diving to his left to turn the French striker's goal-bound shot away for a corner.
Schwarzer was becoming Arsenal's chief tormentor and he denied Aleksandr Hleb from close range on 19 minutes after Fredrik Ljungberg's shot from Henry's cross was blocked by Jonathan Woodgate.
After Boro went ahead, the Gunners stepped up their assault but were again guilty of over playing.
Van Persie went close on three occasions, the best effort being a fizzing 35-yard free-kick that Schwarzer kept his eye on to parry.
The Boro keeper denied Cesc Fabregas on 32 minutes when, in a rare piece of direct play from the Gunners, he took possession just outside the area before almost immediately letting loose with a thunderous drive that Schwarzer blocked.
Arsenal continued to enjoy the lion's share of the possession after the restart but failed to really threaten.
Arsenal went closest on the hour when a trademark Henry early free-kick that was struck immediately on referee Rob Styles' whistle.
As Schwarzer scampered across goal, the Boro keeper was relieved to see the ball bounce wide of the right upright.
The visitors were down to 10 men two minutes later when Styles reached for the red card when George Boateng cut down Ljungberg with the most reckless of challenges.
The Gunners drew level within five minutes. Arsenal had tried so hard to score the perfect goal and in the end the breakthrough came from the penalty spot.
Emmanuel Eboue broke into the right side of the penalty area but was hauled down Stewart Downing.
Up stepped Henry to calmly side-foot the penalty into the left side of the goal with Schwarzer diving the wrong way.
Arsene Wenger then raised the stakes in his quest for all three points with a triple substitution that included debutant Julio Baptista.
Henry went close with a free-kick that shaved the top of the bar on 80 minutes and Gallas fired a shot inches over just seconds later.