Boro's Under-21s were undone by a goal 10 minutes from the end as Arsenal edged a tight PL2 encounter.
Sonny Finch had brought Mark Tinkler's side back on level terms early in the second half after they had fallen behind on 36 minutes.
But they would ultimately leave the capital without a point despite their spirited showing.
The Teessiders started brightly and almost opened the scoring, but Nathan Simpson's effort from long range came back off the post.
Jack Stott also had a shot blocked as Boro looked to make inroads, although they survived a scare at the other end as Jimi Gower's strike went narrowly off target.
The deadlock was broken when Khayon Edwards picked out the bottom left corner for the Gunners.
Boro's response was impressive, with Simpson forcing Arsenal goalkeeper Khari Ranson into action.
At the other end, Edwards was denied a second by a fine Shea Connor save on the stroke of half-time.
A foul on Simpson handed Boro an opportunity to level things up early in the second half, and Finch made no mistake from the penalty spot to do just that.
The game was in the balance and Daniel Nkrumah almost struck what could have been a decisive blow, but the Boro man's header went narrowly over.
The pivotal third goal went the way of Arsenal, with Michal Rosiak hitting home what proved to be the winner in the 80th minute.