The Millers drew 2-2 with the Iron in the first leg at Glanford Park on Saturday but secured a 2-0 victory at the New York Stadium in the return leg to book their spot at Wembley Stadium on May 27.
Three minutes later, Rotherham goalkeeper Marek Rodak kept out Hakeeb Adelakun's powerful low shot, but at the other end, the Millers had a penalty call waved away after Ryan Yates caught Ryan Williams in the box.
Paul Warne's charges went on to dominate proceedings for the remainder of the first half and were rewarded on the stroke of half time when skipper Richard Wood latched on to a long throw-in to head home at the near post.
The restart saw Scunthorpe come out strongly but before long the hosts picked up from where they had left off in the first half and went on to double their lead just after the hour mark.
The visitors went on to miss several gilt-edged opportunities as they briefly threatened a comeback, but suffered a huge setback on 77 minutes when team captain Rory McArdle was shown a second yellow card for a late challenge on Joe Newell.
Scunthorpe lost their momentum thereafter and, save for the odd foray into the final third, were unable to pose much of a threat as the Millers saw out the game to keep their hopes of a swift Championship return alive.
ROTHERHAM UNITED (4-1-4-1): Rodak; Emmanuel, Ihiekwe (Ajayi 52'), Wood, Mattock; Palmer; Williams (Taylor 68'), Towell, Vaulks, Newell (Forde 90'); Smith
SCUNTHORPE UNITED (4-2-3-1): Watson; Vermijl, McArdle, Wallace, Townsend; Yates (Hopper 83'), Ojo; Adelakun (McGeehan 62'), Holmes, Morris; Toney (Novak 81')