The Bandits had been in contention throughout the meeting, four wins from in-form reserve Matej Kus helping to keep the score close at 37-35 with only three races remaining.
But the Panthers pounced at the end to deny The Borderers the chance of victory, or for that matter a losing bonus point.
The home side finished with a flourish, recording 5-1s in heats 13, 14 and 15 to ensure Berwick left the East of England Showground with nothing to show for their efforts.
Lasse Bjerre (13+1) and Ales Dryml (12+2) each dropped only one point for Peterborough, with Ulrich Ostergaard winning three of his four starts.
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For Berwick, David Bellego (9+1) and Kevin Doolan (8) each won a race, with Kus top-scoring on 13.
Team manager John Anderson said: “We just fell short at theend, but again showed we are a team capable of pushing a lot of sides on their own track.”
* Berwick Speedway will utilise their final midweek rain off date on Wednesday, September 10 against Workington Comets with a 7.30pm start.
This was an early season call off at just after 7pm on May 24. With both clubs racing on a Saturday it has proved difficult to fit it in.
Berwick are planning a special cut price deal for this meeting (more details next week).