After a goalless first 45 minutes at St Andrew's, Mikael Forssell gave Blues the lead seven minutes into the second period.
Five minutes later, however, the Gunners were level through James Dunne.
Daniel De Ridder secured all three points for Blues' second string with just 13 minutes remaining.
New loan signing Mauro Zarate completed the full ninety minutes of the match.
Blues: Doyle, Parnaby, Timmins (Wilson 71), Taylor, Pearce, Mutch, De Ridder, Howland (Sammons 90), Forssell, Zarate, McSheffrey.