Former Lincoln striker Lee Thorpe salvaged a last-gasp point for Orient with a 89th minute close-range header.
Lincoln had grabbed the lead 15 minutes from time when giant defender Ben Futcher headed home and looked to have sentenced Orient to their first home defeat of the season until Thorpe's late strike.
In truth, it was a drab Third Division affair that neither side deserved to win. Orient looked to be suffering from a Worthingtonm Cup hangover following Tuesday's victory against QPR and they failed to manage a single strike on target in the first half.
The closest they came to scoring came when striker Gary Fletcher headed inches over early on and then shot wide on the stroke of half time, although he also had a goal ruled out following a push on a defender.
But Lincoln were little better and their only first-half effort on target was a Stuart Bimson free-kick that flew straight into the arms of Orient keeper Glenn Morris.
After the break Orient struggled against Lincoln's physical presence and Orient's teenage keeper Morris had to make a smart stop from Richard Logan at the foot of the post.
But Lincoln's aerial dominance told 15 minutes from time when the giant Futcher headed in Mark Bailey's long throw.
Orient threw caution to the wind, but referee Andy D'Urso turned down their penalty claims after Matthew Brazier went flying before Andy Harris saw his shot saved on 84 minutes, the home side's first effort on target.
In a frantic finish Lincoln keeper Alan Marriot tipped away a free-kick from Billy Jones before the hosts levelled when Jones floated in a cross from the left and Thorpe headed home to get his side out of jail.
After the game Orient manager Paul Brush said: "We didn't play well, but at least we didn't give in. Collectively we were not above average."
While Lincoln manager Keith Alexander was disappointed to lose a goal in the last minute, he reflected: "I would have settled for a point before the game."