Massimo Maccarone was on the scoresheet again, as he equalised for Boro early in the second half. City had taken an undeserved lead late in the first half with a goal from Stephen Ireland.
It was another useful run-out for the Italian who hopes to push for a first team return once he is fully match fit.
A wayward pass by Colin Cooper led to City snatching the points three minutes from time.
Boro team:
Jones, Liddle, Hines, Cooper, Wheater, Doriva, Cattermole, Kennedy (Walker), A Johnson, Maccarone, Craddock (Watling)