Orient slipped to their first defeat in eight games at Glanford Park after a below par defensive showing cost them dearly against a Scunthorpe side fighting for survival in League One.
Akpo Sodje put the visitors in front early on after good work from the influential Mark Duffy and Niall Canavan extended their lead when he headed home a Duffy cross.
Kevin Lisbie gave the O’s hope when he headed in a Dean Cox corner in first half stoppage time, but despite threatening on a number of occasions in a frantic second period, the play-off chasers came away empty handed.
Russell Slade again shuffled his pack as Martin Rowlands returned from a groin injury to the middle of midfield, whilst David Mooney started up front as Shaun Batt shifted to the right and Elliot Omozusi started his first game since returning to the club as he filled the void in the heart of defence left by the injury to Scott Cuthbert.
Orient had the first chance when David Mooney volleyed narrowly wide on three minutes after good work from Romain Vincelot but almost immediately the O’s were behind.
Duffy led the charge from midfield and played in Sodje in the right channel who shot across Jamie Jones and the ball went in off the post.
Orient responded brightly and should have been level within a minute. Dean Cox slipped in Kevin Lisbie to put the leading scorer through one-on-one with Eirik Johansen but the keeper stood up and made a good save to maintain his side’s lead.
Orient were shaken by the early goal but found their rhythm and dominated long periods of the opening 30 minutes though failed to really test the home keeper.
The next major talking point came with 36 minutes gone when Sodje appeared to elbow Leon McSweeney, the goalscorer escaped with a yellow card but most in the ground expected he’d see red.
However six minutes later the O’s were made to pay for not taking advantage of their superiority. Substitute Mirfin switched the play to Duffy on the right who curled a ball in that Canavan rose to meet and glance his header past Jones.
The O’s again responded well to going further behind and right on the stroke of half-time found themselves back in it. Lisbie rose highest to head home a Cox corner to give the visitors some momentum heading into the interval.
Orient started the second half like they finished the first and Cox almost pulled them level on 47 minutes when he found space in the left channel and hit a shot that was well saved by Johansen.
The O’s still did not look entirely comfortable defensively and three minutes later Sodje headed down for Michael Collins who hit a terrific volley that looked to be goal bound but hit the side netting from 20 yards.
It was a game that ebbed and flowed and Orient continued to ask questions of the home defence as David Mooney went close with an awkward shot on 57 minutes that Johansen did well to palm away and then five minutes later he made a super save to deny Cox who hit a rasping drive after good work from Lisbie.
Soon after, the home side were almost out of sight when the ever-dangerous Duffy snaked his way down the right and fired a dangerous ball into the box that Jones did well to push away with Sodje ready to pounce.
As the half wore on, Orient lost their way at times but mounted a late charge deep in injury time when a scramble saw substitute Jimmy Smith have a shot brilliantly saved before MacDonald smashed a follow up across the face of goal but it was not to be as the home side held on to condemn Orient to their first defeat in eight games and mean Monday's match against Bury is a must-win game if the O's are to keep their play-off dream alive.
SCUNTHORPE: Johansen, Reid (C) (Mirfin - 40), Ryan, Sodje, Barcham (Forde - 90), Canavan, Duffy, Nolan, Collins, Newey, Hawley (Alabi - 75)
SUBS: Severn, Ribeiro, Grella, Gibbons
BOOKINGS: Sodje (36), Ryan (65), Alabi (90)
ORIENT: Jones; McSweeney, Omozusi, Clarke (C), Odubajo; Cox, Rowlands (Smith - 75), Vincelot, Batt (Cook - 66); Mooney (MacDonald - 82), Lisbie
SUBS: Grainger, Vanderhyde, Sawyer, James
REF: David Webb
ATTENDANCE: 3,042 (240)