After eight straight league defeats to the Gunners this was a welcome, and long-overdue, win. No wonder the Boro fans were jubilant at the final whistle.
Strikers Yakubu Ayegbeni and Massimo Maccarone - £15,000,000 worth of talent - had the satisfaction of scoring Middlesbrough's first goals at the Riverside Stadium this season.
The defeat was a bitter blow to Arsenal's hopes of mounting a title challenge, particularly after they controlled the first half.
Arsenal could have been two up in the opening minutes and were certainly unlucky to be behind at the interval after Middlesbrough scored with their first on-target shot.
The home side, however, played with more confidence and belief after the break when the Gunners lost their composure and, for a time, their discipline.
The win was a boost for Middlesbrough after a rock-bottom performance in their last home game against Charlton Athletic.
The result enhanced the prospects of Chelsea retaining the Premiership trophy on a day when rivals Liverpool and Manchester United also dropped points.
Yet it could have been all so different for Arsenal if they had taken their chances early in the game.
Jose Antonio Reyes failed to beat Mark Schwarzer and then struck a post with the Australia international goalkeeper well beaten.
Arsenal completely dominated midfield with their inter-passing and movement. Middlesbrough, in fact, struggled to get into the game so it was a complete surprise - and against the run of play - when Yakubu scored his first goal following his £7.5million summer move from Portsmouth.
Yakubu collected a pass from George Boateng with his back to goal and then held off Kolo Toure before shooting low into the corner of the net.
The visitors piled on the pressure early in the second half in search of an equaliser and Reyes had a shot blocked after beating two players.
Teenage debutant Adam Johnson showed plenty of promise and spirit and forced Jens Lehmann to save at the foot of a post.
Maccarone returned to Middlesbrough in the summer after a loan spell in his native Italy. The striker was an expensive flop in his first spell on Teesside, but his game has improved on his return to the Premier League.
The Italian kept his cool as he raced through to slip the ball past Lehmann and shot into the net to increase the lead after 59 minutes.
Middlesbrough, after being second best to Arsenal before the break, took the game to their opponents.
Arsenal were struggling at this stage. They pulled a goal back in added time when Reyes broke through to go round the advancing Schwarzer and score from an acute angle.
The visitors could have snatched a dramatic draw but Ashley Cole shot wide from a misplaced clearance.
Middlesbrough took their chances and overall deserved the points but Arsenal must regret failing to make their first-half superiority count.
Man of the Match: Yakubu Ayegbeni
The Nigerian striker at last started to show why Steve McClaren was prepared to splash out £7.5million for his services during the summer. His pace and power posed a constant threat to the Arsenal defence and his first Boro goal was a deserved reward.