Erik Huseklepp’s last-gasp own goal saw Darren Ferguson’s men seal a 3-2 success and steal the points at Fratton Park.
It was a match-winner which came on the counter-attack deep into stoppage time.
Ryan Tunnicliffe crossed from the left after carrying the ball out of his own half, and the Blues’ Norwegian international accidentally bundled the ball into his own net past Jamie Ashdown.
Up until that point, Pompey had bossed the second half, putting Posh under intense pressure for long periods.
They had already levelled through Benjani 54th-minute equaliser.
Ultimately, though, it was the visitors who collected the triumph at the death.
And Cotterill couldn’t help but feel his side had been hard done by on a cruel night on the south coast.
He said: ‘We played well enough to win that game, that’s for sure.
‘We created that many chances in the second half, we just got caught by the sucker-punch at the end.
‘Now we’ve got the feeling that Blackpool had on Saturday.
‘It’s amazing what this game does.
‘You have the euphoria of a last-minute winner on Saturday and three days later you have to take that.
‘We didn’t deserve that – if we take our chances the game is out of sight, anyway.
‘There was one occasion where they must have had four or five fantastic blocks to stop us scoring.
‘In that second half we dominated. I thought we played some really good football.
‘Unfortunately, the scoreline takes some of the gloss off how we played.
‘If we had come back and won 3-2, everybody would be saying how fantastic we were. But because they get a last-gasp goal it takes the gloss off it for us.’