Played at Cantley Park, the United youngsters did pull the game level at 1-1 before a clinical second-half performance from the hosts saw them run out comfortable winners in the end.
The side found themselves behind after just two minutes though as Max Adamson slotted home beyond Ewan Oxborough to give Rovers the lead after a ball through from Jaiden Campbell-Ryce.
United responded well to going behind and won a penalty after 25 minutes following a foul by Chris Pooley. Charlie Burden-Whittleton stepped up and saw his spot kick saved by Jacob Bryant, but the Scunthorpe forward was fortunate the ball sat nicely for the rebound as he restored parity with the rebound.
The Iron could have gone ahead soon after but for a fine save from Bryant, but it was Doncaster who restored their lead on 29 minutes with Will Green sliding in a Harry Wood cutback.
Rovers could have lead by more at half-time, but Oxborough denied Campbell-Ryce, while Adamson twice hit the upright.
United switched goalkeepers at half-time, with Josh Murtagh replacing Oxborough at the interval and he was to be tested within minutes of the restart as Adamson sent an effort narrowly wide. On 48 minutes, however, he was to be picking the ball out of his net as Adamson made no mistake, meeting an inch perfect cross from Pooley to complete his brace.
The fourth and final goal for the hosts came on 67 minutes when Green's corner was met by Flint and sent into the back of the net. Doncaster could have had more, with a number of chances to follow, with one standout save from Murtagh in particular coming to deny Freddie Allen what looked like a certain goal from his header.
United could have reduced the arrears on 80 minutes when an effort towards the far top corner cannoned back into play off the crossbar.
IRON: Oxborough (Murtagh, 45'), Knight, Abraham, Cunningham, Hill, Cribb, Wallace, Dickinson, Williams (Smaller, 50'), Burden-Whittelton, Harmon (Nicholson, 85').