Darren Ferguson's adventurous side came from behind at struggling Brighton to record their second victory in their last five League games.
Brighton gave debuts to former Stockport left-back Jim McNulty and ex-Oldham striker Craig Davies.
They were two of six signings made by manager Micky Adams during the January transfer window and both were on the score-sheet in the first half but that did not prevent Brighton falling deeper into relegation danger.
Davies put them ahead in the 26th minute, pouncing on the rebound when Peterborough's young goalkeeper Joe Lewis spilled a harmless shot from French winger Seb Carole.
Posh equalised on 38 minutes, top scorer Craig Mackail-Smith rising in between Brighton's central defenders to head his 20th goal of the season from a Paul Coutts cross.
The visitors were ahead four minutes later, Aaron McLean tucking in the rebound after Brighton keeper John Sullivan was at full stretch to get a hand to George Boyd's shot.
Jim McNulty swept in a half-volley from a Carole corner in first-half stoppage time to get Brighton back on terms but the match turned on a controversial 65th-minute penalty.
Isle of Wight ref James Linington penalised Brighton defender Adam Virgo for a challenge on Boyd.
Dean Keates converted the resulting penalty, although Brighton claimed later that replays proved there was no contact.
McLean ensured victory for Peterborough in the 76th minute with his 13th goal of the campaign.
Sullivan got a hand to Mackail-Smith's shot but could not prevent it rolling towards the net and McLean made sure just before the ball crossed the line.