City claimed Yorkshire bragging rights with two goals in a five-minute burst at a chilly Don Valley.
Luke O'Brien, with a thundering first senior strike, and Nicky Law secured another away win to get City firmly back in the mix at the top of League Two.
But keeper Rhys Evans proved just as instrumental by pulling off an unbelievable save from Drewe Broughton, somehow keeping his header out seconds before Law settled matters at the other end.
City took a long while to get going and rode their luck at times in the first half. If Rotherham's finishing had been sharper, Stuart McCall's side would have found themselves two down in the opening five minutes.
But they hung in there and stepped up several gears after the break.
Rotherham still had chances but O'Brien, who had bombed forward throughout, showed them how it should be done with an explosive strike that flew into the far corner after 71 minutes.
Evans and the crossbar then denied Broughton and, less than a minute later, Law beat on-loan Rotherham keeper David Stockdale with a curler from the corner of the box.
The only blot on the day for the 1,637 travelling army was the sight of Paul McLaren limping off after an hour.
CITY: Evans, Moncur, Lee, M Clarke, O'Brien, Osborne, Law, McLaren, Daley, Thorne, M Boulding. Subs: Conlon, Ainge, T Clarke, Nix, McLaughlin.