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Gillingham defender Max Ehmer scored a stoppage-time equaliser on Saturday.
Danny Lloyd had put the visitors ahead in the second half but Gills felt they should have levelled through Josh Parker.
The striker and his team-mates celebrated a goal moments after conceding but the officials claimed it hadn’t crossed the line.
Reaction from Gills boss Steve Lovell after their last-gasp leveller
Defeat was avoided when Ehmer ran onto the ball and fired low past the keeper.
The Gills were without captain Lee Martin, struggling with a calf injury. His solitary strike separated the sides last time they met, in what was Steve Lovell’s first game in charge. Elliott List was called up in his place.
Gillingham were looking to hit back from last weekend’s loss to league leaders Wigan, while protecting an unbeaten home run stretching back seven games.
Peterborough had the best of the early chances, the division’s leading scorer Jack Marriott firing a shot at Tomas Holy in the opening minute. Michael Doughty also tried his luck without success.
The Gills improved with a switch of formation, List moving out to the wing after starting upfront alongside Tom Eaves. He looked to force his way into the box on a couple of occasions, while a dangerous cross was also cleared.
Marriott remained a threat and it needed a good stop from Holy, with his legs, to prevent him scoring late in the first half. Josh Parker had fired well over for the home side.
Like the first half, Peterborough started the second better, with Marriott seeing a powerful effort blocked and strike partner Omar Bogle poking one wide.
It needed a vital block from Max Ehmer to deny Liam Shephard with almost an hour gone, Marriott smashing the follow-up well over the bar.
Bradley Garmston picked Parker out with a cross for the Gills but the striker was unable to get his header on target. Garmston won the hosts a corner moments later that Luke O’Neill bent, wind-assisted, onto the roof of the net.
The visitors took the lead in the 67 minute, Danny Lloyd capping an impressive performance by volleying home from close range off Shephard’s cross from close range.
Gillingham thought they had equalised four minutes later, when Parker followed up on a shot that had been saved by keeper Jonathan Bond, but referee Andy Davies waved play on.
The Gills went for broke in the final 15 minutes, with Conor Wilkinson joining Eaves and Parker upfront.
O’Neill hit a late free-kick into the Peterborough wall but the Gills found an equaliser through Ehmer, racing onto the ball from Tafazolli's clearance and after chesting it down the defender hit it low past Bond.
Gillingham: Holy, O’Neill, Ehmer, Zakuani, Garmston (Ogilvie 72mins), Byrne, Hessenthaler, Reilly (Wilkinson 76mins), List (Wagstaff 68mins), Parker, Eaves. Subs not used: Hadler, Nugent, Moussa, Nash.
Peterborough: Bond, Shephard, Tafazolli, Baldwin, Lloyd (Forrester 89mins), Doughty, Bogle (Morias 66mins), Taylor, Grant, Ward (Hughes 81mins), Marriott. Subs not used: O’Malley, Da Silva Lopes, Kanu, Cooper.
Attendance:7,154 (476 away)