Paul Dickov’s men took the derby day bragging rights as Nathan Tyson returned to the starting line-up to clinch the match-winner at Glanford Park.
New Zealander Rory Fallon had put Scunthorpe ahead in the 24th minute when, following good work from Neal Bishop, he latched onto a beautiful pass to slot into the bottom corner past the despairing left-hand of Jed Steer.
However, just as United looked to be gaining the initiative, the hosts failed to clear a Rovers corner and Doncaster skipper James Coppinger gambled on a loose ball to turn and fire in with Bobby Olejnik helpless in the 29th minute.
Harry Forrester had the chance to make it 2-1 to Doncaster but saw his low drive blocked well by the advancing Olejnik in a one-on-one situation just seconds after Coppinger’s leveller.
The first half had all the ingredients of a derby match with challenges flying in early doors - one of which saw Matt Sparrow go into the book in the seventh minute.
And tempers also flared off the pitch between supporters just as hoardes of police were sent to man the stand behind Olejnik’s net just before the first half ended.
Tyson sparked wild celebrations as he marked his return to the fray with a 49th minute drive after good work from Dean Furman in the build-up.
The Rovers striker was then cautioned by the referee for his overzealous celebrations as Doncaster went in front for the first time in the game.
Coppinger tried to make it three four minutes later but his curling free-kick from all of 25 yards was tipped over comfortably by Olejnik.
Liam Wakefield later forced Scunthorpe into a mistake in the box and managed drive in a low shot, however, Olejnik got down well to deny the defender’s 56th minute effort.
United were guilty of not charging down a surging Forrester who unleashed a powerful strike on goal as the chance sailed wide of the left-hand post.
Scunthorpe reacted through Paddy Madden as he delicately guided a bouncing ball towards Steer’s net with the shot going just wide.
Reece Wabara later tried to catch Olejnik out at his nearpost before Fallon was inches away from collecting his brace and restoring parity for the hosts - but his looping header went over the bar in the 64th minute.
Further chances fell to Coppinger, Richie Wellens and Forrester for the visitors as Scunthorpe cut a frustrated figure on home soil with efforts on goal at a premium.
Substitute Hakeeb Adelakun offered some hope for the home side as he cut inside onto his right but dragged a 77th minute shot wide.
Referee Stocksbridge had the home fans on his back with 11 minutes to spare as Bishop tried to create space for himself before going down in the area. However, the man in the middle waved away the protestations as Doncaster escaped.
United pushed on in a bid to clinch a point at the death, but it was the away side who stopped their rotten run of two back-to-back away defeats in League One, Doncaster taking all three points back to South Yorkshire.
Scunthorpe (4-4-2): 26 Olejnik, 25 Boyce, 33 Brisley, 24 O’Neill, 30 Williams, 12 Bishop, 14 Hawkridge, 28 McSheffrey, 7 Sparrow, 9 Madden, 34 Fallon. Subs: 13 Severn, 3 Dawson, 4 McAllister, 11 Myrie-Williams, 16 Adelakun, 27 Kee, 32 Llera.
Rovers (4-1-4-1): 1 Steer, 6 McCombe, 12 McCullough,15 Wakefield, 22 Wabara, 19 Wellens, 21 De Val, 4 Furman, 26 Coppinger, 10 Forrester, 14 Tyson. Subs: 13 Marosi, 9 Robinson, 18 Keegan, 23 Bennett, 25 Peterson, 31 Lund, 35 Ferguson.
Referee: Sebastian Stocksbridge