In a drama-drenched second-half, Orient grabbed a 51st minute lead through Andy Scott - knowingg that the win would have taken them to the top of the table.
But Scunthorpe hit back with a leveller just 60 seconds later when striker Steve Torpey scrambled the ball home.
But within a minute the visitors had their backs against the wall when defender Nathan Stanton was sent off following an off the ball incident with Orient scorer Scott.
For the last 30 minutes, Scunthorpe hardly emerged from their own half, but defended doggedly to secure a precious point.
The Os had enough chances in the final half an hour to win the game, but Scunthorpe goalkeeper Paul Musselwhite was in fine form as he denied Justin Miller and then Donny Barnard with super stops.
The second-half was in marked contrast to the first, as the top two sides looked nervous and cancelled each other out.
In a disappointing half, the home side just shaded things. Jabo Ibehre wriggled past two defenders, and tested Musselwhite, but the keeper pushed his shot away.
Then Wayne Carlisle fired over from close range, following Matthew Lockwood's left wing cross.
But the visitors should have gone ahead on 31 minutes when Paul Hayes crossed from the left, but Torpey headed over from close range.
Just before the break, Ibehre went close, and that set the pattern for the second half.
Orient Quickly grabbed the lead when Ibehre set up Scott to delicately chip home, but Orient's joy was short lived when Matthew Sparrow's cross was met by Torpey, who gleefully netted.
Referee Paul Merlin then dismissed Stanton for aiming a kick at Scott, and from then on it was backs to the wall.
Ibehre and Carlisle went close as the O's picked up the tempo and the ever dangerous Ibehre almost restored Orient's lead with another teasing effort.
But Scunthorpe substitute Michael Rankine almost won the game in the fourth minute of stoppage time as Orient were caught on the break, but goalkeeper Lee Harrison spared their blushes.