Iron fire blank for fourth consecutive game
The first half was in stoppage time when Wayne Carlisle was bowled over at the end of a good run to win a penalty which he then drove high into the net.
Referee Trevor Kettle ruled that players from both sides had entered the area and ordered the kick to be taken again.
Carlisle held his nerve and this time put his shot low and wide of the keeper's right hand.
It was the Irishman's third penalty this season and it was enough to bring his side only their third league win in a dozen games.
Although the margin was narrow, defeat for Scunthorpe was costly as they picked up five bookings and in the 90th minute had their promising young defender Andy Butler taken off.
He went down beneath a heavy tackle from Pirates teenage striker Lewis Haldane and a badly gashed left foot will rule him out of Scunthorpe's FA Cup replay with Barnsley.
Haldane became one of two Rovers bookings and was subbed right away.
Ray Graydon refused after the game to speculate upon his own future but Chairman Geoff Dunford denied the manager had resigned or been sacked.
He added the board had no intention of buying out the five-year contract they gave Ray Graydon in May 2002.
While the penalty was clear enough the big mystery of the first half was how Rovers escaped going two or three down.
Defenders Kevin Austin and Graham Hyde both gave away kicks around the box for fouls on Steven MacLean and twice he bemused Rovers with his free-kick routines.
The first time he had the ball in the net but referee Kettle ruled it had been taken too early.
Scunthorpe, short of experience as they nurse injuries lost Lee Featherstone with a suspected broken nose in the first half but Paul Hayes proved a good replacement for the former Sheff Utd winger.
The second half was scrappy and desperate. Shots were few, the best for Scunthorpe from Steve Torpey and a late low shot from Paul Hayes which the Rovers keeper did well to cover.