Sam Baldock's two goals in six second-half minutes ended a two-match losing streak for City and bagged their first points on the road this term.
Baldock will have gained great satisfaction from taking his tally to four goals this season - the first coming courtesy of a short back-pass from Mark Little.
The recalled marksman was heckled by the home crowd after a protracted move from MK Dons fell through last summer, with the 23-year-old insisting he rejected the move and Peterborough claiming they backed out of talks.
Regardless, Baldock's goals pile the pressure on a Peterborough side who were already experiencing their worst-ever start to a league season, with Lee Tomlin's injury-time penalty mere consolation.
Home chairman Darragh MacAnthony gave manager Darren Ferguson a vote of confidence earlier in the day.
But Ferguson would have been less than impressed with his side's defending, just three days after conceding five at Burnley.
Ferguson reshuffled his backline with three new faces from the weekend, Nathaniel Knight-Percival coming in for his league debut along with Gabriel Zakuani and Kgosi Ntlhe.
Marvin Elliott, one of three Robins changes, was recalled for his first start in seven months having recovered from a ruptured Achilles tendon, Albert Adomah the surprise omission.
The majority of the 5,435 present at London Road were on their feet after just 25 seconds as Tomlin's long-range effort nestled into the side-netting.
George Boyd fired over soon after for Peterborough amid what was a positive start from both sides, although, despite plenty of promise, neither goalkeeper had been tested come the half-hour mark.
Stephen Pearson poked narrowly wide at the near post from the lively Baldock's cross before Nathaniel Mendez-Laing threatened at the other end.
Adomah replaced Cole Skuse at half-time following what appeared to be a serious injury to the midfielder, although the change was held up after the second half was delayed by around five minutes due to one of the assistant referees falling ill.
When the action finally resumed goalkeeper Robert Olejnik produced a fine stop to tip Baldock's effort around a post.
But Baldock finally got the goal he deserved in the 56th minute, capitalising on Little's error before rounding Olejnik and slotting home.
Little was lucky to stay on the pitch just minutes later following an awful challenge on Liam Fontaine.
Yet the hosts were indeed soon facing a uphill battle after Baldock made it two-nil with a simple finish from Adomah's right-wing pass.
Peterborough were losing their self-control and Tyrone Barnett was lucky to escape red for a dangerous challenge which saw Greg Cunningham stretchered off.
Tomlin, having been brought down by Martyn Woolford, reduced the arrears from the spot amid eight minutes of injury time, but City were left celebrating their fifth win in six league visits to London Road.
