The points are valuable in Arsenal's quest for a Champions League place but their manager Arsene Wenger must not have been happy with the display of his team.
Arsenal lacked the class and hunger of their recent performances.
Middlesbrough have been cruelly hit by injuries this season and there was another blow shortly before the kick-off.
Goalkeeper Mark Schwarzer suffered a back injury in the warm-up and fellow Australian Brad Jones was hastily called up for a rare first-team opportunity.
Manager Steve McClaren just had time to call up the teenage midfield player Adam Johnson for a place among the substitutes.
It meant Middlesbrough had no reserve keeper on the bench.
Boro hoped to boost their challenge for a UEFA cup spot next season while the Gunners were keen to record their seventh win on the trot.
Following a 5-3 win at Highbury in the early part of the season the Gunners were strong favourites for the double.
Lauren was booked for a foul on home winger Stewart Downing after only two minutes.
Middlesbrough were the first to threaten danger when Jimmy Floyd Hasselbaink pulled the ball back for Doriva. The Brazilian midfield player unleashed a powerful shot that just grazed the outside of the post.
Arsenal played at a slow tempo and surprisingly failed to trouble the inexperienced Jones before the break.
Three minutes from the interval Franck Queudrue was booked for a foul on Jose Reyes. The Middlesbrough defender protested his innocence but really he could not complain over a yellow card.
Middlesbrough had battled hard in the first half but Wenger could not have been happy with the performance of his team. Jones had not even had a shot to save.
For the second half the Gunners brought on Dennis Bergkamp for the injured Reyes.
Downing was having a rather subdued game for Middlesbrough. The highly talented local boy has not been at his best in recent games and will no doubt benefit from a holiday next week.
Boss McClaren wants Downing to recharge his batteries with a well earned break after a hectic schedule.
Arsenal were not showing the urgency of a side chasing the number two spot in the Premiership. They never looked in danger of losing but there was a lack of penetration from their attack.
The Middlesbrough defence battled hard with George Boateng a powerhouse in midfield.
There is no question that Middlesbrough have missed the midfield aggression of the former Aston Villa player in recent weeks.
Thierry Henry was having a quiet game for Arsenal and not revealing the blistering form that brought him hat tricks in two successive games.
Bergkamp had a go but was high and wide with his shot.
After 73 minutes Arsenal finally made the breakthrough when Robert Pires scored with a left-foot shot from seven yards.
An attempted Queudrue clearance struck Doriva and fell perfectly for Pires to beat Jones with a left foot shot.
It was a blow to Middlesbrough especially as Hasselbaink had a glorious chance for an equaliser shortly after.
The former Leeds United striker broke through and should have claimed his 15th goal of the season in a one on one situation with the goalkeeper.
Jens Lehmann saved however and Hasselbaink flung himself to the ground in anguish.
Hasselbaink also blasted a shot wide of the near post as time ran out.
Boro sent on substitutes Daniel Graham and Ugo Ehiogu in the final minutes, but there was to be no rescue act.
Man of the Match: George Boateng – The powerhouse midfielder did his best to help keep Arsenal at bay and showed that his presence has been missed in the Boro engine room.