United took the lead twenty minutes into the second half but Boro fought back and leveled through substitute Danny Graham with just ten minutes left.
Tom Craddock won the game, converting a penalty, after he was brought down in the box with seven minutes left to play.
Robert Huth came through the 90 minutes unscathed but Malcolm Christie was replaced early in the second half after another knock on his ankle.
Boro team:
Turnbull, Hines, McMahon, Huth, Bates, Kennedy, Owens, Goulon (Walker), Christie (Graham), Craddock, Johnson.