The Iron had led thanks to a smart move that culminated in Rory Fallon’s low finish from the edge of the area, but were unable to hold onto their lead.
James Coppinger’s first half equaliser and an early second half strike from Nathan Tyson proved enough to claim victory.
Doncaster managed to see the game out to claim three points, despite United throwing a lot of bodies forward towards the end.
The Iron went into the game looking to make it four wins from their last five home matches and also move within a point of their visitors.
Both sides were clearly up for the local derby with the challenges flying in from the very start, Matt Sparrow going in the book for an early foul.
Scunthorpe were being roared on by a crowd of over 5,000 and the fans were in full voice from the first whistle.
The visitors were unwilling to roll over and let United have it all their own way, flying out of the blocks at the start.
Bobby Olejnik was forced into a flying save after little over a minute, diving to save Richie Wellens’ powerful drive and tip it over the bar.
Doncaster continued to attempt to assert their authority on the game, but were wasteful in front of goal, missing a couple of good chances.
Harry Forrester fired straight at Olejnik and Nathan Tyson also headed into the ‘keeper’s gloves when well positioned.
As the half grew the Iron started to get into the game and were getting a lot of joy from their left hand side, with Gary McSheffrey looking particularly dangerous.
Paddy Madden and strike partner, Rory Fallon were both looking menacing too and the former had a great chance to give the Iron a 20th minute lead.
The Irishman managed to turn the ball towards the goal, but found visiting ‘keeper Jed Steer at his acrobatic best to turn it around the post.
Steer was left stranded for the Iron’s opener though as the impressive Fallon finished a well worked Scunthorpe move.
A cross-field switch found Neal Bishop who rolled it into the path of McSheffrey, before he reversed it to Fallon who fired a precise drive past Steer from 18 yards.
The Iron’s 24th minute lead would only last just over five minutes as the goal spurred the visitors into life, with James Coppinger levelling the scores.
Doncaster had a corner that sparked a scramble in the Iron box, with the ball eventually falling for Coppinger who fired home on the spin.
It could have been much worse for the Iron as Forrester raced clear only to find Olejnik standing firm on the edge of his box.
Both sides were trying to gain control of a match that was becoming very frantic and end to end, with last gasp defending at either end keeping it level at 1-1.
Doncaster started the second half just like they did in the first, pressuring the Iron from the first whistle with an instant reward.
A great exchange between Dean Furman and Nathan Tyson saw the latter race clear of Luke O’Neill before firing past Olejnik in the 49th minute.
Doncaster were nearly celebrating just a minute later, with the home ‘keeper once again at his best to tip over his crossbar.
Russ Wilcox tried to address this by bringing on Jennison Myrie-Williams for Terry Hawkridge in an attempt to inject some pace into the side.
It nearly paid instant dividends as good play down the right involving Myrie-Williams ended in Rory Fallon guiding a header just over the bar.
The visitors were still asking most of the questions though as Shaun Brisley, on his home debut, was required to be alert to prevent the opposition on numerous occasions.
A well worked move saw Richie Wellens find himself in the box, but the Peterborough loanee was on his toes to snuff the danger out.
As the game entered the final 15 minutes, Wilcox rolled the dice again, bringing on Hakeeb Adelakun for Gary McSheffrey, trying to force and equaliser.
The Iron were throwing bodies forward to try and salvage a point, but Doncaster were proving a match for whatever the hosts could throw at them.
A series of hopeful balls were fired towards the box, but the Iron were unable to create any real chances from their crosses.
The visitors were able to comfortably see the game out for a big three points and leave the Iron empty handed.
Scunthorpe United: Olejnik, O’Neill, Boyce, Brisley, Williams, Hawkridge (Myrie-Williams, 62), Bishop, Sparrow, McSheffrey (Adelakun, 73), Madden, Fallon.
Substitutes not used: Severn, Dawson, McAllister, Kee, Llera.
Doncaster Rovers: Steer, Wakefield, McCullough, McCombe, Wabara, De Val (Keegan, 82), Coppinger, Furman, Wellens, Forrester, Tyson.
Substitutes not used: Marosi, Robinson, Bennett, Peterson, Lund, Ferguson.
Attendance: 5,420 (1,728 away).