Following a fairly even start to the game at Underhill, the Gunners took the lead on 26 minutes through Ignasi Miquel but their lead was short-lived as Blues were level just two minutes later when Jacob Rowe headed home from a corner.
Arsenal regained their one goal advantage when Oguzhan Ozyakup fired home from an acute angle just moments before the half time whistle.
Blues started the second half brightly and twice came close to equalising with long range efforts from Ashley Sammons and Robin Shroot respectively.
However, on 52 minutes Nacer Barazite made it 3-1 for the hosts with a well taken solo effort.
Second half substitute Luke Rowe had Blues' best chance of reducing the deficit just after the hour mark but his effort was well saved by Arsenal keeper Vito Mannone.
Arsenal Res: Mannone, Yennaris (Anga, 70 mins), Miquel, Cruise, Evina, Eastmond, Ozyakup (Bytes, 70 mins), Henderson, Barazite, Murphy (Deacon, 57 mins), Freeman. Subs: Shea, Edge.
Blues Res: Taylor, Preston, Vignal, Tainio, Murphy, Jacob Rowe, Shroot, Mutch, Asante, Sammons, Barnet (Luke Rowe, h/t). Subs: Daniels, Ozturk, Ntambwe, Kerr.