Andy Campbell gave City a 1 - 0 half time lead when he scored in the 38th minute. Campbell was then taken off 2 minutes later to be replaced by Stuart Fleetwood.
City doubled the lead 9 minutes into the second half when Michael Simpkins scored direct from a 20 yard free kick.
Orient pulled one back to become the first team to score against the reserves since August but their revival was short lived as Jason Bowen twisted and turned in the 6 yard box and scored the decisive third goal.
City lined up
Margetson, Green, Collins, Simpkins, Giles, Dimond, Hamilton, Bonner, Leo FW, Campbell, Bowen.