The 2-2 draw still leaves the Yorkshire side with every expectation of taking part in the end-of-season play-offs as they are six points clear of seventh-placed Tranmere Rovers with five game to play.
But they blew a two-goal lead at Brisbane Road. Robert Snodgrass had scored both for the visitors, but Sean Thornton and Simon Church netted to earn Orient a point.
Brighton boosted their hopes of survival in Tuesday night's only other game, as they beat Hereford United 2-1 at Edgar Street. The Bulls are 11 points from safety, and appear certain to go down along with the bottom club Cheltenham Town.
Goals from Tommy Fraser and Lloyd Owusu put the Seagulls in control, with Kris Taylor getting a late consolation for the home side.