Alan Knill's side now need just four points to get back to nought points after the former Derby County defender headed a 44th minute winner in an entertaining local derby.
The game set off at a blistering pace and was rewarded with two goals inside a minute.
Scunthorpe opened the scoring on six minutes. A quick corner on the right caught the Rotherham defence flat-footed, with Dave Mulligan whipping an inswinging cross in for Billy Sharp to glance into the bottom corner.
But 60 seconds later Rotherham - who were deducted 10 points at the start of the season - were level following a stunning volley from Eugen Bopp.
The 22-year-old, on a one-month contract at Millmoor to prove his fitness, caught Steve Foster's misplaced header on the volley from 25 yards out and the ball flew into Joe Murphy's bottom right hand corner.
Will Hoskins, Rotherham's match winner at Blackpool last week, crafted a chance for himself moments later when he won the ball from Mulligan, but he lofted his effort over the bar.
Rotherham were enjoying the majority of the possession and should have completed the comeback when Ritchie Partridge was played in on the right by Michael Keane, but the former Liverpool winger hurriedly blazed wide.
After Hoskins curled a close effort over the bar on 36 minutes, Rotherham finally got their noses in front after a well worked free-kick.
Lee Williamson took it short to Hoskins 25 yards from goal and his cross to the back post was headed back across the goalkeeper by the unmarked Mills.
Brian Laws made two changes in the second half to try and turn the game Scunthorpe's way and it almost paid off as Sharp burst clear and rounded Neil Cutler, but his left foot effort was superbly blocked by David Worrell.
Williamson had a golden opportunity to seal victory for the Millers on 61 minutes when he met Partridge's cross with a flying header, which was parried by Murphy.
Williamson stormed in to meet the rebound but blasted the ball at Murphy and the ball deflected to safety.
Matt Sparrow then missed an open goal in the dying moments when he stretched to meet a cross but blazed over.