Both teams fielded teams made up of under 15 and 16 players and it was the City youths who triumphed thanks to a Jack Redshaw hat-trick and two goals from the impressive Ahmad Benali.
The Blues led 4-0 at half time and Redshaw completed his treble on 73 minutes to make it 5-0 before the Shakers claimed a late consolation.
The victory now guarantees the Blues second place in the Division One West table and sets up a play-off semi final against league winners, Morecambe.
If successful against Morecambe, the young City side would take on either current champions, Nottingham Forest or Hartlepool United in the play-off final.
Details of the semi final play-off are still yet to be decided.
The two clubs meet again this afternoon at Radcliffe Borough FC (2pm kick-off) in the final group game of the Manchester Senior Cup.
City:
Clegg, Robinson, Chantler, Wabara (Smith 59), Paldan, Carter, Grandison (Bunn 54), Benali, Hulme, Redshaw, Elabdellaoui (Kapsolopadus 59).
unused subs: Johanssen.
