Goals from Britt Assombalonga and Tommy Rowe gave Peterborough a deserved 2-0 victory at the expense of the Gills.
Assombalonga, whose 94th-minute strike earned the Posh a point at Priestfield in December's two-all draw, opened the scoring from close range on 42 minutes, before Rowe doubled their advantage with a stunning strike shortly before the hour mark.
Manager Peter Taylor opted for the 4-2-3-1 formation that worked so well at MK Dons last month; as a result, Amine Linganzi
replaced Adebayo Akinfenwa in the only change from Saturday's starting line-up.
However, unlike the defeat against Rotherham United, the Gills started brightly. Cody McDonald
found Myles Weston
who, in a similar position to where he scored from at the weekend, sliced his effort wide.
Despite a recent run of form that saw them lose four of their previous six league fixtures, the Posh are in the play-off places for a reason. Defender Jack Baldwin nearly headed them in front in the 14th minute, but Stuart Nelson
produced a reaction save to deny him from Danny Swanson's corner.
Taylor was called into an early substitution immediately after, as on-loan Crystal Palace defender Ryan Inniss had to be replaced by former Peterborough player Charlie Lee
This was only Inniss' second game back after suffering a hamstring injury in the defeat against Sheffield United in February.
Lee slotted in at centre-back, but the Gills needed a great block from Amine Linganzi
to prevent Nicky Ajose from breaking the deadlock at the back post on 17 minutes.
Nelson made another good save midway through the first half to deny former Gills player Jack Payne, who shot from 25 yards out, before catching Assombalonga's on-target header with ease.
McDonald came close with a low shot from an acute angle that was parried by Bobby Olejnik, and just when it seemed that a goalless first half was on the cards, the Gills fell behind three minutes before the break.
Swanson's cross was deflected by Kgosi Ntlhe, and Assombalonga hooked the ball in with his left foot for his 30th goal of the season.
Linganzi made way for Akinfenwa at the break, as the visitors switched to a 4-4-2 formation, and the swap nearly paid dividends straight away.
The powerful forward shrugged off Payne in the centre of the park, and found McDonald in space. The Gills' leading scorer attempted to chip Olejnik, who just managed to tip the effort over the bar.
Nelson denied Swanson, Conor Washington shot wide under pressure from Michael Harriman
and Ntlhe came close with a back-heeled effort before Rowe hit an unstoppable 25-yard shot that cannoned off the Gills' bar and across the line to make it 2-0.
The scoreline could have become even more unpleasant in the 64th minute, when Steven Gregory
was adjudged to have clipped Assombalonga just inside the box.
However, after picking himself up from the floor, the Peterborough striker casually side footed his penalty into the hands of Nelson.
Gills' best chance of the half fell to Martin with a free-kick on the edge of the box after McDonald was fouled by Swanson challenging for a header, but the left back lifted his effort over the bar.
The move of the match nearly resulted in the home side putting the result beyond any doubt on 79 minutes.
Swanson intercepted a loose pass from Connor Smith, ran 30 yards, then found Ajose who put through the unmarked Assombalonga. However, Nelson was there once again to deny him.
Washington looped a header onto the top of the bar from Ajose's cross in the final 10 minutes, as Gillingham's record of one win in 35 years at London Road showed little sign of improving.
The Gills are on the road once again on Saturday, as they make the short trip to east London to face Leyton Orient in an all-ticket fixture.
Attendance: 6, 543 (Gillingham 254)
Gillingham: Nelson, Martin, Barrett, Inniss (Lee 15), Harriman, Gregory, Hewitt, Weston, Linganzi (Akinfenwa 46) Dack (Smith 66), McDonald
Subs not used: Baxter, Fagan, Hessenthaler, Birchall
Peterborough: Olejnik, Ntlhe (Alcock 83), Nugent, Baldwin, Little, Payne, Rowe, Swanson, Ajose, Assombalonga, Washington
Subs not used: Day, Brisley, Bostwick, Conlon, Vassell, McQuoid
Goals: Assombalonga (42), Rowe (58)
Bookings: Barrett (36), Martin (90)
Referee: Mr D Whitestone