On-loan striker Anthony Shandran touched home the winner 20 minutes from time to give York City's promotion hopes a major boost.
The visitors found themselves under pressure for most of the second half but Shandran flipped home Jon Parkin’s mammoth throw to send Orient crashing to only their fourth home defeat.
It was rough justice on the home side as York keeper Michael Ingham pulled off second-half stops from Gary Alexander and Lee Thorpe - while Matthew Lockwood and Andy Harris also went close for the home side.
But the O's failed to make the most of their domination and after the game York boss Terry Dolan said: "It was a hard-earned win but the players produced another tremendous performance.
“We had to withstand some tremendous pressure and deserved the little bit of luck that went our way." Orient boss Paul Brush was not so happy. "It was very frustrating,†he said.
“We had plenty of possession in the second half but were done by a bit of a smash and grab." Brush kept his players in the dressing room for more than 30 minutes after the match and added: "There were a few home truths said in there." The game had started at a frantic pace with both sides hitting the woodwork in the first eight minutes.
First Alexander flicked on a throw from Harris and Lockwood fired against the post and he then saw his follow-up effort cleared off the line.
At the other end York striker Parkin rattled the Orient bar with a speculative 25-yard drive.
Alexander also had an effort ruled out for offside in the first few minutes while home keeper Scott Barrett made a smart stop from City's Lee Nogan.
After that blistering start the game went off the boil as the two sides cancelled each other out.