Edin Dzeko partners the Argentine, with Carlos Tevez on the bench, while Laurent Koscielny comes into the Gunners' defence with Thomas Vermaelen missing from the squad
Aguero suffered a knee injury in the first game of the season against Southampton but begins the game alongside Edin Dzeko in attack, who scored against Real Madrid in the Champions League in midweek.
Scott Sinclair also starts for City, who are without Samir Nasri due to a hamstring injury. Joleon Lescott returns to the defence ahead of Matija Nastasic, while Pablo Zabaleta replaces Maicon at right-back.
Arsenal, meanwhile, are missing central defender Thomas Vermaelen, who is reportedly ill. Laurent Koscielny partners Per Mertesacker at the back.
Gervinho is expected to continue in attack ahead of Olivier Giroud, while Aaron Ramsey is preferred to the likes of Alex Oxlade-Chamberlain and Theo Walcott in midfield.
Manchester City: Hart; Zabaleta, Kompany, Lescott, Clichy; Garcia, Yaya Toure; Silva, Aguero, Sinclair; Dzeko.
Subs: Pantilimon, Kolarov, Nastasic, Barry, Rodwell, Tevez, Balotelli.
Arsenal: Mannone; Jenkinson, Mertesacker, Koscielny, Gibbs; Diaby, Arteta; Ramsey, Cazorla, Podolski; Gervinho.
Subs: Martinez, Djourou, Santos, Coquelin, Walcott, Oxlade-Chamberlain, Giroud.