Peterborough defender Sagi Burton was sent off in the last minute of the first half as Portsmouth struggled to overcome the second division's bottom club.
First division leaders Portsmouth went on to complete their sixth successive win in all competitions but they did not often show the class or the fire power which has taken them to the top of the first division.
Burton was shown a red card by Surrey referee Lee Cable on the advice of his flag-waving assistant after Burton had appeared to raise his elbow towards the face of Bulgarian international striker Svetoslav Todorov.
Angry Peterborough manager Barry Fry had to be led back to his seat along the touchline by stewards after a furious clash with the referee.
Until then Peterborough had been coping comfortably with subdued Portsmouth and were unlucky to be trailing to a 26th minute goal.
Paul Merson created it with a centre from the left and although Mark Burchill saw his close-range header brilliantly saved by Mark Tyler the rebound fell into the path of Nigel Quashie to score from three yards.
Quashie went close again for Portsmouth but for Peterborough Helgi Danielson and Neale Fenn should have levelled.
Peterborough's cause was not helped when busy midfield player Tony Shields was taken off on a stretcher after a first-half collision with Richard Hughes.
Peterborough strove desperately for an equaliser after the break but it was Portsmouth who went further in front with a goal in the 76th minute when Linvoy Primus scored from four yards, converting a centre from the right by Todorov.
After the second goal Peterborough showed signs of conceding several more but Tyler showed impeccable handling and made a great one-handed save to deny Kevin Harper in the 81st minute