A first-half goal from John Martin and a late disputed penalty converted by Matthew Lockwood left United still looking for the first win of the season, and ensured that the East London outfit won their second succesive game.
Orient were never at their fluent best as Scunthorpe worked tirelessly denying the home side space.
In a game of few clear-cut chances Orient hot head Jamal Campbell-Ryce was always a handful down the right but he wasted the home side's first chance after 21 minutes with a shot from a tight angle when a cross would have been better.
Scunthorpe almost took the lead when inspirational skipper Peter Beagrie drifted a free-kick just wide of the post while at the other end, Dean Smith scuffed a good chance following Lockwood's corner.
The O's broke the deadlock with a goal out of the blue after 38 minutes when Martin slid home from a tight angle after Lee Thorpe caused panic in the visiting defence as they allowed the ball to drift into the danger area.
After the break, the game, in stiffling conditions, threatened to boil over with a rash of bookings and Scunthorpe almost levelled when Beagrie curled a free-kick just over the bar.
The former Premiership star went close with another free-kick that brought an excellent save from Orient's on-loan goalkeeper Rhys Evans before the home side wrapped things up with a disputed penalty nine minutes from time.
Referee Paul Rejer pointed to the spot when Campbell-Ryce appeared to slip in the area.
Lockwood thumped home his second spot kick of the season and after the match visiting manager Brian Laws refused to comment on the incident.
But even Orient manager Paul Brush conceded: "I didn't think it was a foul."
Brush added "We didn't play as well as we could have but it's nice when you win even if you're not on the top of your game."