The Shrimps’ hopes of a fifth consecutive victory ended with their first league defeat of the season at the Globe Arena.
Goals from Liam Kelly and Jordan Bowery handed the visitors three points with Kevin Ellison’s goal little more than consolation for Jim Bentley’s side.
The result might have been disappointing for the home camp but, while the home fans were upset at defeat, referee John Brooks came in for the greater criticism for some increasingly bizarre and pedantic decision-making.
A scrappy opening saw both sides struggling to retain possession, though it was the Shrimps who gradually took early control.
Cole Stockton saw an effort flash wide of Alex Cisak’s right-hand upright before their best first-half opportunity came on 19 minutes.
Ellison was played in behind the visitors’ defence but his right-footed effort was pushed away by Cisak.
Stockton had another effort blocked before the visitors took the lead with the half-hour approaching.
Bowery’s shot was deflected behind for a corner which the Shrimps failed to clear fully.
Possession eventually found Kelly, 25 yards out, and he curled a shot past Barry Roche, though the keeper wasn’t helped by the ball skidding off the wet surface.
Kelly was off target from 18 yards moments later as the visitors sought a second goal with Gavin Massey curling an effort wide on the counter-attack.
Jack Dunn had a shot blocked and Stockton an effort easily saved as the opening half drew to a conclusion with the visitors in front.
Roche was forced into early action after the break, pushing out Robbie Weir’s deflected effort before the Shrimps drew level.
The ball found Ellison 20 yards out and his first-time shot flew past Cisak to bring Bentley’s players on level terms.
Roche denied Bowery when he got behind the home defence but could do nothing moments later when Bowery’s shot deflected off Whitmore and wrongfooted the keeper.
Bentley rang the changes in response with Rhys Turner and Alex Kenyon introduced to the fray but it was the visitors who came closer to scoring again.
Roche was forced into a hat-trick of saves, keeping out headers from Tom Parkes and Yvan Erichot, as well as Bowery’s effort at his near post.
There was still time for Paul Mullin to make a late appearance off the Shrimps’ bench but, despite his cameo and Ryan Edwards ending the game as an emergency centre-forward, they could not fashion a late leveller.
Morecambe: Roche, Wakefield, Edwards, Whitmore, McGowan, Fleming (Kenyon 63), Rose, Barkhuizen, Dunn (Turner 63), Ellison, Stockton (Mullin 86). Subs: Nizic, Molyneux, Massanka, Jennings.
Leyton Orient: Cisak, Hunt, Parkes, Erichot, Kennedy, Cornick, Kelly, Weir, Massey, Bowery, McCallum. Subs: Sergeant, Palmer, Nnomo, Semedo, Pollock, Koroma, Judd.
Referee: John Brooks.