James Morrison curled a beauty past Arsenal goalkeeper Jens Lehmann following a one-two with Jason Euell to give Middlesbrough the lead against the run of play.
New signing from Chelsea William Gallas was at fault for the opening goal, though too were much of the Arsenal back line.
Despite Arsenal's early pressure there was little penetration and Boro' were only too happy to take advantage.
Once behind Arsenal turned up the tempo and forced 'keeper Schwarzer into several fine saves.
The game turned on George Boateng's sending off following his second yellow card.
With Middlesbrough under the cosh, Stuart Downing tripped Arsenal full-back Eboue in the box and the referee pointed to the spot.
Thierry Henry coolly converted the spot-kick and Arsenal sensed all three points were in the offering.
But for all their pressure, the Gunners simply could not penetrate the Middlesbrough back line.
Jonathan Woodgate, making his debut following his season's loan from Real Madrid, marshalled the 'Boro defence superbly and showed no signs of the injuries that have plighted his career so cruelly in recent years.
With the game there to be won, Arsenal gave a debut to their recent recruit from Real Madrid Julio Baptista.
The Brazilian powerhouse certainly adds a bit of muscle to the Gunners' midfield, something lacking since the departure of the heralded Patrick Viera.
But the South American was unable to help prise open 'Boro as Arsenal's efforts became more frenzied.
The game was in remarkable contrast to last year's fixture, when 'Boro were on the receiving end of a 7-0 hammering.
The result leaves Gunners' boss Arsene Wenger with a headache following just two points from the opening three fixtures.
