It halted a run of four successive defeats for the home side as the in-form Londoners found themselves beaten for the first time in eight games.
Scunthorpe got off to a flying start when striker Akpo Sodje fired them into a fourth-minute lead with his sixth goal in 12 games since joining the club from Preston.
He squeezed a shot low into the far corner after being played free into the box by Mark Duffy.
Orient came roaring back with a spell of good pressure and could have been back on level terms when striker Kevin Lisbie broke free into the box, only to be denied by the legs of keeper Eirik Holmen Johansen.
It was against the run of play when Scunthorpe went 2-0 in front in the 42nd minute when centre back Niall Canavan headed home a right-wing cross from Duffy for his sixth goal of the campaign.
But deep into first-half stoppage time, Orient got themselves back into the game when Lisbie headed home a right-wing corner from Dean Cox.
The Londoners pressed strongly throughout much of the second half, looking to revive their hopes of gatecrashing the play-offs.
Scunthorpe were forced to defend doggedly but were also indebted to young keeper Holmen Johansen, on loan from Manchester City.
He pulled off a couple of early second-half saves, each time to deny winger Dean Cox. And in stoppage time he rescued Scunthorpe again with vital stops from Orient substitutes Jimmy Smith and Charlie MacDonald.
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- Kevin Lisbie