From the ensuing spot-kick Holt blasted home what proved to be the winner in an often ragged and untidy encounter, but three more precious points, courtesy of Holt, hoisted Shrewsbury into second spot in the League Two table.
The first half brought little to enthuse over as Shrewsbury were restricted to long-range efforts, while Rotherham's main source of pressure were the long throws of Andy Nicholas.
After the break the home side continued to have the greater share of possession, without looking particularly dangerous, but gained a numerical advantage when Broughton was sent off in the 59th minute.
Worse was to follow for the Millers in the 69th minute when Stockdale pulled down the advancing McIntyre who had raced onto a through ball from Holt.
When McIntyre went crashing, Stockdale was immediately shown the red card and a substitution by Rotherham boss Mark Robins resulted in young goalkeeper Steven Cann facing Holt's penalty.
But Shrewsbury's record signing made new mistake from the spot and, just as he had done in Shrewsbury's previous home match against Dagenham & Redbridge ten days ago, clinched another win for Paul Simpson's side who extended their unbeaten league run to seven matches.
With Rotherham down to nine men Town had opportunities to win by a greater margin, but Cann denied skipper Ben Davies with a fine diving save, while Holt missed the chance of adding to his goal tally, when he headed wide from close range.