Orient striker Lee Steele grabbed a hat-trick to bring Lincoln's eight-match unbeaten league run to an end. The Red Imps were in the lead five times but could not hold out as Orient fired in two late goals to take them back up to second place in the table.
Lincoln opened the scoring in the second minute when centre-back Gareth McAuley climbed above the Orient defence to head home a corner from Francis Green.
The O's got back into the game in the 11th minute when a cross from Wayne Carlisle picked out Stuart Wardley at the far post. The midfielder sent his header against the bar but Steele followed up to score from close range.
Lincoln got their second of the game three minutes later when a mistake by Orient defender Alan White let in Simon Yeo who went onto score his fifth goal of the season.
Green then went close with a long-range effort which was blocked on the line by Orient keeper Lee Harrison.
Things were level again in the 37 minutes when a cross from Michael Simpson found Jabo Ibehre and the striker volleyed home. Orient keeper Harrison was lucky to escape with a yellow card after bringing down City striker Martin Carruthers as he headed the goal but Lincoln went on to hit their third goal of the game after Yeo was brought down by Justin Miller on the edge of the box. Kevin Sandwith sent the free kick into the box and McAuley got in front of his marker to head home.
Lincoln then had chances to go further in front. Sandwith released Green with a 40-yard pass but the striker's shot brought a diving save from Harrison.
13 minutes from time Steele headed home a Lockwood free-kick. Steele then went on to get his third goal of the game a minute from the end when Lincoln were caught out pushing forward.