Stockport were quick out of the blocks and Anthony Pilkington fired an early effort just over.
Orient, always on the back foot, were forced into a re-shuffle when winger John Melligan injured himself sliding in on Gareth Owen and was replaced by debutant Jack Jeffrey, on loan from West Ham.
The visitors, sharper throughout the first half, were rewarded for their endeavours on 13 minutes when Rowe's corner from the left hit defender Saah and bounced into the net.
Orient responded and Jason Demetriou saw a free-kick deflected wide, but County posed the biggest threat and home keeper Glenn Morris saved well from Rowe's header.
Michael Raynes then hit the Orient bar with a looping header.
Orient's top scorer Adam Boyd missed a glorious chance to level on 33 minutes and County cashed in when they scored a second before the break.
Pilkington delivered a free-kick from the right and McNulty's powerful header exploded into the net.
After the break Orient tried to force their way back into the contest and Adam Chambers looked to have been bundled over in the area but referee Robert Shoebridge waved away their penalty claims.
But County were always a threat on the break and Morris pulled off another smart stop from Pilkington.
Any comeback hopes were finally extinguished 20 minutes from time, when County substitute Stephen Gleeson found the impressive Rowe and he swivelled and fired into the far corner of the net from 16 yards.