A Robert Pires goal boosted Arsenal's chances of securing an automatic Champions League place. The Frenchman made the most of his good fortune when the ball bounced in to his path in a packed penalty area and he slotted home from close range.
It was a rare chance for Arsenal, who often found themselves defending a swift Boro counter-attack.
In the first half, Boro's Dorivo clipped the bar, while Jimmy Floyd Hasselbaink wasted two late chances.
And Boro's failure to equalise condemned them to a record of losing both home and away to Arsenal for the last three seasons.
Their afternoon had started badly when keeper Mark Schwarzer was injured during the warm-up and Brad Jones had to take his place.
And Brazilian midfielder Dorivo - making only his second start since Christmas - was unlucky to see his shot off the outside of his boot clip the top of the bar.
Ray Parlour and full-back Stuart Parnaby were combining well, but the pair were caught out when Jose Antonio Reyes tricked his way past them.
The Spaniard cut the ball back for Thierry Henry, but his shot was wildly off target - though he later went close with a cheeky, chipped effort.
Boro ended the half in the ascendancy as Jens Lehmann flapped - not for the first time this season - at a succession of corners.
Then Parnaby and Parlour worked well in tandem to set up Szilard Nemeth, but his shot was blocked by Lauren, who scrambled to cover for Kolo Toure.
Earlier, Toure had headed Henry's free-kick over the bar.
Arsenal brought on Dennis Bergkamp at half-time for Reyes, but to little effect.
The hosts continued to favour the counter-attack and allow Arsenal the majority of possession.
Given the visitors' lack of creativity, it did not look a terrible tactic.
But then Boro's organisation and discipline was undone by an unlucky break.
After a pinball passage of play, the ball squirmed free to Pires, who tucked the ball away from close range.
Boro had their chances to equalise - with the best falling to Hasselbaink.
He should have scored after Phillipe Senderos gifted him the ball, but he scooped his shot into Lehmann's arms.
The Dutch striker was equally tame with a headed effort before that as Boro lost ground in the race for Europe.
Middlesbrough manger Steve McClaren:
"It was a magnificent performance, my lads were heroic. They kept their shape and executed the game plan perfectly. "How we've lost that game, I don't really know. A ricochet and a lucky goal stopped us keeping a clean sheet.
"We never gave Arsenal a chance, we hit them on the break and we had chances and we could have won the game."
Arsenal manager Arsene Wenger:
"We needed to be patient and then Robert Pires scored the goal that got us the three points. "Middlesbrough played well, they were disciplined and very cautious. We did make one mistake at the back but our keeper kept us in the game.
"But considering the possession, if one team deserved to win, it was us."
Middlesbrough: Jones, Parnaby, Riggott, Southgate, Queudrue, Parlour (Ehiogu 90), Doriva (Graham 86), Boateng, Downing, Nemeth, Hasselbaink.
Subs Not Used: Cooper, Kennedy, Johnson.
Booked: Queudrue.
Arsenal: Lehmann, Lauren, Toure, Senderos, Cole, Fabregas, Vieira, Silva, Pires, Reyes (Bergkamp 45), Henry.
Subs Not Used: Van Persie, Cygan, Almunia, Eboue.
Booked: Lauren.
Goals: Pires 73.
Att: 33,874
Ref: P Dowd (Staffordshire).
MMIX
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