Joey Dawson scored a hat-trick, while Harry Lewis notched the other goal as the side returned to winning ways in the Youth Alliance League, building on their positive performance away at Grimsby Town last weekend.
They had to do it the hard way though as they turned around a 1-0 deficit at the interval and it wasn't until the final ten minutes of the game when the scoreline became a more positive one.
Professional Phase Development Coach Steve Thornber said: "It was a tricky surface to play on, particulary with the rain we had over the weekend.
"In the first half, Rotherham showed a lot of desire to close down and they were very direct into their number nine and we struggled to come to terms with that. Having said that we started the game quite well.
"At half-time, we changed things round a little bit and started much better. It was good to get back to winning ways."
The first chance fell to the Iron after three minutes when Dawson was played through in on goal, but the 'keeper made a good one-v-one save.
On 15 minutes, Patrick Virgo found space on the wing to send in a cross for Dawson. He was again denied by the home shotstopper.
Just past the 20-minute mark, the hosts went ahead as Jake Balme was beaten from a Millers effort - a goal which would send the side in 1-0 up at the interval.
On 54 minutes, Dawson did get the Iron back on level terms, finally beating the Rotherham United goalkeeper. He was slipped in down the side and deservedly fired into the net to restore parity.
Eleven minutes later, the scoreline was turned around. Harvey Cribb slotted Dawson through on goal, with the forward looking to take the ball around the goalkeeper. He was subsequently brought down and, althought the card was yellow for the foul, the referee promptly changed the colour to red following foul and abusive language from the Rotherham shot stopper.
The delay from the penalty award didn't deter Dawson, who dusted himself down to covert the penalty to put Scunthorpe ahead for the first time.
With an extra player and now in the lead, the Iron continued to dominate proceedings and could have added to their scoreline. Oliver Lobley saw his header saved by the replacement goalkeeper, while Cam Wilson had a few chances throughout the second half.
Harry Lewis replaced Lobley just past the hour-mark and he took 22 minutes to get in on the act. His goal came on 84 minutes after being slotted into the area on the left side, turning his defender inside-out and gaining a couple of yards of space with a neat Cruyff turn before firing into the top right corner of the net with his right foot.
The hosts, now 3-1 down and a man light, did try to convert a consolation, but their half-chances were dealt with well by the Iron, who would go onto keep a clean sheet in the second half.
The scoring was complete on the stroke of full-time, with Dawson getting his second treble of the season. It was, once again, a breakaway for him as he was played through, rounding the 'keeper before putting the ball into the top corner.
The Iron are next in action on Saturday, December 12th when they play host to Bradford City at Brumby Hall (11am kick-off). Please note, in line with COVID guidelines, spectators are not currently permitted at these games.
IRON: Balme, Baker, Dawson, Gallimore, Kemp, Lobley (Lewis, 62), Virgo, Wilson, Young, Moore, Cribb.
IRON UNUSED SUBS: Foster, Griffin, Strouther.