Paddy Madden won the game for the visitors, with a close range finish mid-way through the opening period.
Three changes were made from the defeat against Sheffield United, with Jordan Clarke, David Mirfin and captain Stephen Dawson coming in for Scott Wiseman, Charlie Goode and Kyle Wootton respectively.
Elsewhere, Luke Daniels started between the sticks, with Clarke and Mirfin joining Niall Canavan and Scott Laird in a four man defence. Dawson came into the midfield alongside Jack King and Neal Bishop, with Tommy Rowe, Madden and Luke Williams retaining their places in attack.
United were the first to register an effort on target, inside of five minutes. After pinching the ball in midfield, Dawson drove at the Doncaster backline and picked out Madden in the penalty area. Unfortunately though, the Iron striker could only sting the palms of Rover 'keeper Thorsten Stuckmann.
Mark Robins' side had the better of the opening exchanges, but they survived a scare in the 17th minute when Nathan Tyson burst through on goal. The attacker evaded two challenges before bearing down on Daniels' goal, however the Iron stopper got out quickly to avert the danger.
Soon after though, the visitors were rewarded for their bright start to the game. After keeping the ball alive from a corner, Rowe whipped in a dangerous ball, which evaded everyone in the box. Everyone apart from Madden, who stole a yard at the back post and then had the simple task of tapping home from close range.
Madden's strike was no more than the Iron deserved after their positive and sharp opening to the game.
The goal did little to change the pattern of play, and the visitors continued to apply pressure. 10 minutes before the break, Rowe had a great opportunity to double the lead, but he could only stab King's cross into the hands of Stuckmann from six yards out.
Darren Ferguson's men almost got themselves back into it on the stroke of half-time through Tyson. However, the attacker's near post effort could only find the side netting of Daniels' goal.
Tyson's attempt would turn out to be the last of the opening period, and in truth it was one of the rare occasions in which the visitors were troubled throughout the half.
The visitors nearly made the perfect start to the second half, when Madden looped the ball over Stuckmann and into the back of the net. But despite the celebrations from the travelling Iron supporters behind the goal, the Irishman was deemed to have been in an offside position when he received Rowe's pass.
After making his first start for over four months, captain Dawson was replaced just after the hour mark by Jamie Ness.
Robins' side weren't being put under any sort of considerable pressure until a flurry of efforts 20 minutes from time. Firstly, full-back Cedric Evina flashed a shot marginally past Daniels' far post from a very tight angle. And then James Coppinger forced the United 'keeper into a smart save with an acrobatic effort from the edge of the area.
Former Iron loanee Dany N'Guessan was introduced with 15 minutes remaining, and he had a chance to level things up soon after coming on. The forward found a pocket of space on the right flank, but he could only drag his shot harmlessly wide of Daniels' goal.
Evina, who went close with an effort earlier on in the half, did so again with 5 minutes to play. This time the defender popped up at the back post, but he could only direct his header wide of the goal.
The hosts' best chance came as the clock ticked past the 90 minutes. Substitute Cameron Stewart was found in space on the left hand side of United's penalty area, before unleashing a curling shot which clipped the crossbar on its way over.
After surviving the late scare, the Iron held out for a vital three points and with it, a confidence boost ahead of the two upcoming clashes with Rochdale and Wigan Athletic.
Doncaster Rovers: Stuckmann, Lund (Stewart 53), Evina, Butler, Williams, Tyson (N'Guessan 76), Taylor-Sinclair, Grant, Coppinger, Middleton (Keegan 46), Alcock.
Substitutes not used: McCullough, Chaplow, Mandeville, Marosi.
Scunthorpe United: Daniels, Clarke (Wiseman 85), Laird, Mirfin (Goode 69), Canavan, King, Dawson (Ness 62), Bishop, Rowe, Williams, Madden.
Substitutes not used: Anyon, van Veen, Henderson, Wootton.
Attendance: 8,744 (1,238 away).