Graeme Lee grabbed the vital three points with a thunderbolt of a shot, but the game then boiled over into an 18-man brawl.
Referee Colin Webster had blown for a late tackle by James Coppinger on Ian Baraclough and shown him a straight red card while Scunthorpe's Steve Torpey, on the pitch for less than ten minutes, retaliated on Coppinger and also saw red.
The game had never appeared to have engendered that kind of conduct, in fact for long periods it was an easy-paced derby, especially in the first half which totally lacked any real passion.
That was due to some sterling work in the Rovers rearguard by Mark Albrighton and Nick Fenton who had some excellent all-round support while ex-Rovers man Steve Foster had a steady debut for The Iron.
Andy Keogh and Billy Sharp went closest for the opposition in the first half with Rovers' best effort coming from Paul Green.
Scunthorpe made a switch at the break, and within three minutes substitute Jim Goodwin stooped low to head home Michael Rose's cross from the left.
For a time it was Scunthorpe in the driving seat, Keogh on two occasions went close to adding to the tally, but then Rovers hit back.
A long and deep speculative free-kick by keeper Alan Blayney saw the ball collected by Michael McIndoe and there was no challenge as he tucked home a 63rd minute equaliser.
That shook Scunthorpe and Tom Evans had to be alert to deny Green and Sean Thornton, while Keogh turned a 30-yard shot into Blayney's hands.
As the game appeared to be heading for a draw, Rovers came up trumps with a last-gasp winner when Lee thumped the ball home.
The seconds were ticking away when the game erupted following Coppinger's tackle on Baraclough and Torpey's retaliation which brought the inevitable red card.