In a pulsating clash played at a frantic pace on occasions, a keenly fought game was settled in the final 10 minutes.
Lee Frecklington put the Millers in front from the penalty spot when referee Mark Haywood ruled that defender Michael Nelson had handled in a tussle with Alex Revell, who also appeared to have his shirt pulled.
Kieran Agard then put the result beyond doubt with a second goal deep into stoppage time. Goalkeeper Jon McLaughlin ran to the opposition penalty area to try and force an equaliser when Bradford were awarded a corner, but the visitors' defence cleared the danger and Agard broke away pursued by the 'keeper to slot into an empty net.
The Bantams thought they had scored twice in first half with a header from striker James Hanson and a Garry Thompson strike, but the former was judged to have pushed defender Claude Davis in the back and the latter ruled offside.
Rotherham's best effort of the opening period came in the 36th minute when McLaughlin made a superb save to keep out Revell's point-blank header at the far post.
Towards the end of a scrappy first half littered with free-kicks, Bradford's assistant manager Steve Parkin was sent to the stands for comments made to the fourth official.
The win puts the Millers into third place on goal difference in League Two, whilst Bradford are still to secure their play-off spot with two games remaining.