Will Vaulks' thunderbolt and Kieffer Moore's 10th of the season sealed victory, the Millers' fifth successive three points at the AESSEAL New York Stadium.
In an open first half, both sides could have gone ahead. First, Rotherham's Richie Towell teed himself up for a volley which Matt Gilks had to palm away and then Anthony Forde forced another good save.
Millers goalkeeper Richard O'Donnell then had to be alert to keep out Paddy Madden's close-range header.
The opening goal came in the 37th minute with Vaulks finding space and blasting an unstoppable 25-yarder into the top corner.
Scunthorpe started the second half with purpose and Conor Townsend came agonisingly close with his effort striking the outside of the post.
Ryan Williams cut in from the left flank and forced a diving save out of Gilks as Rotherham pushed for a decisive second.
It came after 71 minutes when David Ball found Moore at the back post after he had dashed swiftly through the Scunthorpe defence.