Efe Sodje's injury-time equaliser kept Bury's hopes of an automatic promotion place alive.
Rotherham took the lead eight minutes from time when referee Jon Moss spotted an offence in the box after Mark Hudson had floated in a free-kick.
Bury's Brian Barry-Murphy was booked and Reuben Reid stepped up to slot home the spot-kick.
With time almost up, Barry-Murphy swung in the corner for the unmarked Sodje to head past keeper Andy Warrington.
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Rotherham: Warrington, Tonge, Sharps, Fenton, Green, Cummins (Jason Taylor 72), Mills, Hudson, Broughton, Clarke (Ryan Taylor 46), Reid.
Subs Not Used: Cann, Burchill, Joseph.
Booked: Green.
Goals: Reid 83 pen.
Bury: Brown, Haslam, Futcher, Sodje, Buchanan, Bennett, Jones, Dawson, Barry-Murphy, Hurst (Jevons 66), Bishop (Morrell 78).
Subs Not Used: Baker, Racchi, Rouse.
Booked: Jevons, Haslam.
Goal: Sodje 90.
Att: 2,890
Ref: Jon Moss (W Yorkshire).
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