But it was a hugely disappointing afternoon for Tranmere who had striker Jose Baxter sent off as they crashed to their first defeat in six games.
Striker Mustafa Tiryaki twice put the visitors in front in a promising start to the game. He opened the scoring after five minutes following a mistake by goalkeeper Sam Slocombe, and netted again after 32 minutes with a terrific strike into the top corner from the edge of the box.
Scunthorpe's first equaliser came after 20 minutes with a header by centre-back Shane Duffy from a free-kick by Michael O'Connor.
They were level again before the interval with a terrific left-foot strike from Bobby Grant.
The game turned sour for Tranmere in the second half when Chris Dagnall converted after a long clearance from Slocombe had split the Tranmere defence.
The visitors were then reduced to 10 men after 62 minutes when Baxter was red-carded for a challenge on home skipper Sam Togwell.
Scunthorpe made sure of victory five minutes later when Grant netted the second goal of the game from the penalty spot, taking his season's tally to eight, after O'Connor had been brought down in the box by Ian Goodison.