Karl Bermingham opened the scoring for the hosts on 20 minutes but new signing Njazi Kuqi scored his first goal in Blues colours to equalise just after the break.
The home side's winner came from substitute Ishmael Miller ten minutes from the final whistle.
The result saw Asa Hartford's second string regain pole position in the Barclays Premier Reserves League (north) table.
Man City: Ronald Waterreus, Danny Warrender, David Sommeil, Paddy McCarthy, Sam Williamson, Ian Bennett, Stephen Ireland, Micah Richards, Marc Laird, Christian Negouai, Karl Bermingham. Subs: Michael Johnson, Kasper Schmeichel, Carlos Logan, Ishmael Miller, Kelvin Etuhu.