Rovers, who had John Oster and Quinton Fortune sent off in the second half, were in control from the start and went ahead through Martin Woods' early penalty.
They had to wait until just after the hour mark to double their lead when Billy Sharp headed home a Woods free-kick.
But the game turned on the dismissal of Oster and Scunthorpe rallied with their numerical advantage, Cliff Byrne heading them back into the game.
Then in the second of six injury-time minutes, Woods handled in the area and Grant McCann hit the spot-kick home to earn a point.
The draw leaves Rovers with just one win from the past nine, while Scunthorpe stretch their unbeaten run to four league games.
Doncaster made the brighter start and their fast, one-touch passing was causing Scunthorpe some trouble from the start.
Mark Wilson had a low drive go just wide of the post and it was another slick passing move that saw Rovers take the lead in the 13th minute.
Oster, Woods and Sharp all interchanged passes around the Scunthorpe penalty area and when the ball fed into Jamie Coppinger, he was taken down from behind by Jordan Spence.
Woods stepped up to fire the resulting spot-kick past Joe Murphy.
Rovers continued to press and Coppinger fired over from eight yards after a fine piece of work from former Scunthorpe striker Sharp and then Woods flashed a 25-yard effort just wide.
Scunthorpe, who were disrupted by having to make two substitutions inside the opening 35 minutes, offered little as an attacking force, with Sam Togwell's header their only real effort on goal.
And in first-half injury time, Rovers should have doubled their lead when Woods slipped Coppinger clear on goal but his low drive was saved by the feet of Murphy.
Scunthorpe were much-improved in the opening exchanges of the second period but they could not create any telling chances and Doncaster doubled their lead just after the hour mark.
Coppinger was brought down on the right wing and Woods curled in a wicked free-kick that Sharp rose to meet and powered a header home to register his first goal for the club.
Scunthorpe were then given a glimmer of hope when Rovers were reduced to 10 men after Oster was given a straight red card for an off-the-ball incident on McCann.
And they soon made the most of their numerical advantage when Byrne headed home McCann's corner with 19 minutes remaining.
Glanford Park was rocking as Scunthorpe went all out for the equaliser.
Byrne, Paul Hayes, Josh Wright and Gary Thompson all had good chances to earn a point, but Neil Sullivan saved well on two occasions.
Doncaster's battle for a win was made even tougher when Fortune was dismissed for a challenge on Byrne, and they could not hold on, with McCann having the last say from 12 yards after Woods had charged down a corner with his arm.