United won a penalty in the fifth minute after Josh Robertson was brought down in the penalty box. Harrison Poulter stepped up to take the spot-kick, taking a good penalty far to the goalkeeper's left, but their tall shotstopper pulled off a brilliant save, diving full length to keep it out.
Then, just two minutes later, Scunthorpe won a free-kick which Harry Lewis took and bent over the wall towards the top corner, and the Rovers goalkeeper dived full length to keep the ball out with another brilliant save.
Shortly after, a ball was played long over the top of the Iron defence and Oliver Lobley turned to run back and deal with it, but collided with their centre forward as he got his feet tangled up but was shown a red card, which left the Iron with an uphill challenge for most of the fixture.
Nevertheless, the Iron went in front on 20 minutes when Lewis sent in a cross from the left-hand side following a corner, playing a great ball into the far post. Their centre-back slipped and missed the ball, with it reaching Tyrell Sellars-Fleming at the far post, who passed it into the back of the net.
There was another good chance on 25 minutes following a goalmouth scramble after a wide free-kick. The ball came to Sellars-Fleming at the far post, and his shot was saved by the goalkeeper.
With 42 minutes gone, Scunthorpe made it two following a short corner which had been worked on the previous day at the training ground. Lewis played a lovely ball into the far post, which Robertson headed into the back of the net.
Doncaster changed shape at half-time and got back into the game within five minutes of the restart. An inswinging free-kick was sent in and saved by Jake Balme, but it came back into the area again and Doncaster finished to make it 2-1.
It then became 2-2 on 72 minutes from a corner. The first phase of the corner was cleared to the edge of the box but then an away player received the ball unmarked on the edge of the box and controlled the ball before half-volleying in the leveller.
The last goal came on 81 minutes after a right-wing cross was sent into the box and there was a scramble at the near post before Rovers tapped it home amidst big question marks about offside.
Academy manager Tony Daws said: "It's a massive learning curve, because down to 10 men for effectively 90 minutes (with stoppage time included) against a side that always has a good academy, we managed to take the lead. We tired in the second half because of the extra man after putting so much into the first half, looking heavy legged.
"We did well but the disappointing thing is we could have defended our box better against crosses, free-kicks and corners coming in. It's something to learn from and try to do better in that same situation next time."
IRON: Balme, Cribb, Lewis, Young, Moore, Lobley, Moore-Billam (Elliott-Bell, 70), Franklin, Sellars-Fleming (Burden, 68), Poulter, Robertson.
IRON SUBS NOT USED: Foster, Wallace, Strouther.
"We did well but the disappointing thing is we could have defended our box better against crosses, free-kicks and corners coming in. It's something to learn from and try to do better in that same situation next time."
IRON: Balme, Cribb, Lewis, Young, Moore, Lobley, Moore-Billam (Elliott-Bell, 70), Franklin, Sellars-Fleming (Burden, 68), Poulter, Robertson.
IRON SUBS NOT USED: Foster, Wallace, Strouther.