The Crystal Palace defender, making his first start, was struck by a shot from team-mate Craig Morgan with the ball flying into the opposite corner of the net past a completely wrongfooted City goalkeeper Donovan Ricketts.
Trying to bounce back from the previous weekend's setback at home to leaders MK Dons, Posh were again caught cold after just 11 minutes when Paul Evans' powerful free-kick was met by Kyle Nix, who was on trial at London Road in the summer of 2006.
The youngster ghosted free of his markers to glance a header inside goalkeeper Mark Tyler's right-hand post.
City could easily have had a second within 90 seconds, home defender Morgan just managing to head a swirling cross from Joe Colbeck away from a lurking Peter Thorne.
All Posh could muster in response was a tame effort from George Boyd that Ricketts watched sail well wide.
The City 'keeper had to be on his toes near the break, punching away a Jamie Day corner before snatching the ball after David Wetherall took the sting out of an overhead kick from Craig Mackail-Smith.
Posh did not seriously trouble Ricketts until after the break when he needed two attempts to hold a Boyd shot as Dean Keates challenged.
But Ricketts was punished for a second fumble on 57 minutes when he failed to gather a Keates shot and Aaron Mclean pounced to grab his 19th goal of the season from close range.
The Bradford goal was subjected to almost constant pressure in the closing stages with Hughes rattling the crossbar from 20 years as Posh forced a succession of corners.
It still looked like ending all-square until that dramatic 88th minute twist.