It came following a clumsy challenge just inside his own box by Kieran Charnock, who was making his first appearance since January in a patched up Peterborough defence.
He felled Scunthorpe full-back Marcus Williams in the game's decisive moment which left his manager Darren Ferguson shaking his head in disappointment.
"It's big decisions which can win or lose football matches and this was a big decision that we got wrong," he groaned.
Earlier there had been little to test either goalkeeper in a lacklustre first half from both teams.
Peterborough did have a golden opportunity to get themselves back on level terms just five minutes into the second half with a good link-up between their normally proficient front pair.
Aaron McLean got behind the home defence and squared an inviting ball low into the box for fellow frontman Craig Mackail-Smith, who somehow failed to apply the finishing touch.
Peterborough continued to have plenty of possession but struggled to break down a Scunthorpe defence in which teenager Krystian Pearce had a good debut on loan from Birmingham.
In the closing stages it was the home side who missed the chance to finish comfortable winners.
First Gary Hooper and then Garry Thompson lifted shots over the top with only keeper Joe Lewis to beat.
Substitute Ian Morris also went close with a shot that Lewis did well to turn behind.
But in stoppage time, Peterborough might have snatched a point when a mistake by Scunthorpe keeper Joe Murphy presented McLean with a half chance which he blazed over from an angle.