Both teams had made sweeping changes but despite plenty of industry from Arsene Wenger's young side - with Alex Oxlade-Chamberlain again producing an impressive display - it was big-spending City who had the edge as £35million Argentina striker Aguero slotted home with seven minutes left following a sweeping counter-attack.
Gunners striker Park Ju-young, who scored in the last round against Bolton, forced City`s reserve goalkeeper Costel Pantilimon to make a brilliant reaction save to his left. The 6ft 8in keeper was called into action again after 27 minutes when the Romanian - on a one-year loan from Poli Timisoara - made another acrobatic one-handed stop to push away Oxlade-Chamberlain's fierce 20-yard strike which was heading for the top corner.
Edin Dzeko then glanced what was a decent chance wide before City opened the scoring with Aguero producing a finish worthy of their multi-million pound attack to win the tie.
Arsenal sent on Russian playmaker Andrey Arshavin for Oxlade-Chamberlain in the closing stages as the home side searched for an equaliser but there was to be no fightback.