Disconcertingly for Rotherham, who are in a play-off place, City looked better equipped on this evidence.
Peter Taylor's arrival has invigorated things and this was a third win from five, including away wins at two of the top seven, leaders Rochdale and now Rotherham.
This win looked, however, to have slipped through their fingers when Adam Le Fondre drilled home his 25th goal of the season after a penalty rather harshly awarded for handball against Steve Williams in the first minute of stoppage time.
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But with the game into its fourth added minute, James Hanson won it with a looping header from a corner.
"He has missed some sitters along the way but got two great headers as well now," said Taylor of Hanson. "He is a handful for the opposition, he is keen and wants to improve and that's always a good thing."
City's new manager said he was "very pleased" with the way his side had played.
"I think it would have been harsh had we not won although I must say Rotherham did have some good chances," said Taylor.
"But we had some, too, and, overall, we played really well and looked dangerous from our corners."
Taylor gave a debut to midfielder Adam Boulder, signed on loan from Millwall the day before. "Adam helped us, calmed us down and on that pitch, when you mustn't let it affect you, he was calm."
Calmness was not something that could be used to describe the emotions of Rotherham counterpart Ronnie Moore.
"People have to do their jobs and an individual hasn't done his in the last minute and their lad has got the winner," said Moore. "How he was allowed a free header, I don't know. We can't keep defending like that and expect to get promotion."
Bradford opened brightly but Williams and Hanson missed excellent chances.
Then Rotherham saw Nick Fenton have a header cleared off the line and left-back Gavin Gunning hit the bar.
Michael Flynn's well-taken 64th minute goal following a run from Gareth Evans was deserved. But Rotherham hit back aided by the introduction of Marcus Marshall for Nicky Law, whose performance was unrecognisable from those he made at Bradford last season.
Marshall saw a header cleared off the line and then he set up a great chance which Danny Harrison blazed over.
Rotherham United: Warrington; Lynch, Mills, Fenton, Gunning (Green, 70); Law (Marshall, 64), Walker, Harrison, Ellison; Pope (Taylor, 79), Le Fondre. Unused substitutes: Annerson, Joseph, Cummins, Roberts.
Bradford City: Glennon; Ramsden, Williams, Clarke, Threlfall; Bullock; Boulder, O'Brien; Evans, Hanson, Flynn. Unused substitutes: McLaughlin, Bateson, Daley, O'Leary, Boulding, McCammon, Oliver.
Referee: A Haines (Tyne and Wear).
Man of the match: Michael Flynn.
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