First half goals from Akpo Sodje and Niall Canavan were enough to see off Russell Slade's side despite Kevin Lisbie's goal four minutes into added time at the end of the first period.
A series of fine saves from Eirik Holmen Johansen in the closing stages ended a run of four successive defeats.
United took the lead inside four minutes after Sodje calmly passed the ball into Jamie Jones' right hand post.
Sodje collected the ball on the right-hand side before laying the ball back to Mark Duffy. The Iron winger then played a succession of passes with Sodje before the final pass freed the former Sheffield Wednesday striker who kept his composure to score his sixth goal of the season.
The visitors could have equalised instantly after Martin Rowlands freed Kevin Lisbie, however, United goalkeeper Johansen - who is on loan from Premier League champions Manchester City - denied the vastly experience striker on the edge of his box.
Scunthorpe could have doubled their lead half way through the first half. Duffy sent a floating ball into the box which Jones was forced to palm behind.
Duffy sent in the resulting corner intended for Paul Reid, however, he was beaten to the ball by a diving Orient 'keeper who punched the ball out of the area.
United's first goal scorer Sodje became the first man into the referee's notebook after a late challenge on the East London's Leon McSweeney.
Five minutes from the end of the first half Reid was forced off and replaced by David Mirfin after suffering a suspected back injury.
Two minutes after the forced substitution Mirfin started a move that brought up their second goal of the match.
The Sheffield born defender played a ball across the face of goal to Duffy who picked out Canavan whose glancing header went in off the post.
United saw their lead halved on the stroke of half time as Lisbie headed Dean Cox's corner into the far post.
Substitute Mirfin was initially penalised for pulling back an Orient's Lisbie on the edge of the box which led to Rowlands taking a free kick which was deflected off of the wall and behind for their fifth corner of the game.
The Iron then had goalkeeper Johansen to thank for preserving their lead two minutes into the second half when he saved Cox's close range shot.
The Norwegian goalkeeper parried the ball directly to the feet of Cox but Mirfin was on hand to clear the ball out of the box.
Five minutes after the restart, Michael Collins had all the Iron fans on their feet after his shot from 25 yards rippled the netting.
Unfortunately for the 3,000 United supporters in the ground the celebrations came too early as his shot whistled past the goalkeeper and post.
Minutes later the visitors came close to restoring the Iron's two advantage. Karl Hawley played the ball across to Sodje who was beaten to the ball by Romain Vincelot who almost put the ball on to the roof of the net.
With just over an hour played Johansen was forced into his first real save of the match. Lisbie, who was surrounded by three United players, laid the ball off to Cox on the edge of the area but his shot glanced the fingertips of the Iron 'keeper and went behind for a corner.
After pressure from the visitors United countered down the right-hand side. Duffy played the up the right wing for Sodje, who then played a through ball to the overlapping winger who was now in the box.
He played the ball across the face of goal intended for Alabi, who had only been on the pitch a minute, but he collided with Jones and the referee brought the game to a holt.
As the fourth official showed there were to be a further five minutes to play, Orient threw bodies forward in search of a late equaliser.
Cox sent in a corner from the right which was spilt by Johansen, however, the United defence held strong to ensure they remained in the lead.
Johansen was then forced into a fine fingertip save from Cox - who's shot was heading for the bottom corner. The resulting set piece caused the Iron supporters to become rather concerned, however, a combination of Ryan, Mirfin, Collins and Sodje ensure the ball was cleared to safety.
Scunthorpe United: Johansen, Nolan, Canavan, Reid (Mirfin, 40), Newey, Duffy, Ryan, Collins, Barcham (Forde, 90), Sodje, Hawley (Alabi, 74)
Substitutes not used: Severn, Ribeiro, Grella, Gibbons.
Leyton Orient: Jones, McSweeney, Vincelot, Cox, Lisbie, Clarke, Odubajo, Rowlands (Smith, 74), Omozusi, Batt (Cook, 69), Mooney (MacDonald, 81)
Substitutes not used: Grainger, Sawyer, James, Vanderhyde
Attendance: 3,042 (240 away).