The Royals went into Tuesday night's fixture having won nine matches in a 10-game unbeaten run and looked like they might extend that sequence when Noel Hunt put them ahead.
However, quickfire goals from George Boyd and Tyrone Barnett gave Peterborough the half-time advantage and Paul Taylor made sure of all three points for Posh late on as they recorded successive league wins at home for the first time since August.
Darren Ferguson's team edged further away from the bottom three while Reading stay in the automatic promotion places after third-placed West Ham could only draw 1-1 at home to play-off chasing Middlesbrough.
Captain Grant McCann and defender Gaby Zakuani were passed fit to enable Ferguson to name an unchanged side.
Midfielder McCann limped out of the defeat at Ipswich on Saturday with a calf strain while Zakuani has been playing through the pain barrier for several weeks now but once again recovered sufficiently from his ongoing toe problem.
Reading were also unchanged after midfielder Jem Karacan overcame a knock resulting from a heavy tackle at Barnsley at the weekend.
Jobi McAnuff and Mikele Leigertwood were just off target for Reading early on.
McCann responded for Peterborough but his crisp 20-yarder was straight at Adam Federici.
Reading went ahead after 20 minutes following a superb piece of individual brilliance from Jimmy Kebe.
The Malian produced a sublime turn out on the left and ran into the box, hitting a shot that Paul Jones could only parry into the path of Hunt.
It was almost immediately 2-0 but Jones got his fingertips to Karacan's effort from the edge of the box.
Peterborough equalised against the run of play in the 25th minute.
McCann's deep corner was headed back across goal by Shaun Brisley and Boyd lashed the ball home.
Nine minutes later, from another McCann corner, Posh went ahead. Barnett lost his marker and powered a header high into the net giving Federici no chance.
Federici then had to get down well to save from Lee Frecklington and Lee Tomlin before half-time to keep Reading in the game.
Barnett came close to grabbing his second goal of the game on the hour when he smashed a shot against the near post following a flowing Peterborough attack.
Shortly afterwards, an Ian Harte free-kick looked like sneaking in at the near post before a defender's leg got a crucial touch to divert the ball away.
Leigertwood then had a presentable opportunity midway through the second half but missed the target from inside the box.
As Reading continued to push for an equaliser, they were hit on the break.
A long ball forward saw Taylor beat Harte for pace before sliding the ball underneath Federici.
Substitute Simon Church, Kebe and McAnuff all tried to reduce Reading's arrears but no-one tested Jones in the Posh goal.