Phil Parkinson said referee Mark Haywood's decision to give Rotherham a penalty was "beyond a joke" following Bradford's defeat.
Lee Frecklington put the Millers in front from the spot in the 79th minute when Haywood ruled that defender Michael Nelson had handled in a tussle for the ball with Alex Revell.
Kieran Agard then put the result beyond doubt with a second goal in stoppage time, yet Parkinson was still smarting at the earlier incident.
He claimed that his player had been "blatantly pushed" in a challenge that "knocked him off his feet".
"I cannot describe what I have just seen on the DVD," said Parkinson after Tuesday's loss. "It was an incredible decision. You compare that with the penalty we didn't get at Chesterfield on Saturday. It is an absolute disgrace.
"The linesman has surely seen that it was a push. It was an incredible mistake.
"Rotherham came with a 4-5-1 formation which made it a scrappy game. They made it difficult for us with the extra man in midfield, but we did not create much in the second half, in all honesty.
"The result rests on small margins and, unfortunately for us, the small margins have come down to a referee's decisions.
"Fortunately for us, the league table has not changed too much and now we have got to prepare for the visit of Burton on Saturday and not feel sorry for ourselves.
"We are still in the box seat and we want do well on Saturday and put pressure on those teams behind us. If we win on Saturday we have got a great chance."