According to the Blues boss, fourth official Alan Young agreed that it was a ‘wrong’ decision.
Referee Thomas Bramall awarded the visitors a 24th-minute penalty following Ronan Curtis’ challenge on Nesta Guinness-Walker, which was converted by Ollie Palmer.
It was an awful decision, ensuring the match official was booed by the home faithful for the remainder of the game.
Pompey came back to claim a 2-1 triumph through goals from Michael Jacobs and Marcus Harness.
Meanwhile, Cowley insists the fourth official told him he also didn't agree with his colleague over Wimbledon’s spot kick.
He told The News: ‘I have watched it back, it wasn’t a penalty, the referee has got that one wrong.
‘The fourth official told me at the time that it definitely wasn’t a penalty.
‘I moaned about referees last week, I was determined that, regardless of the result, not to speak about them after this game because I want the focus to be on the players and also our supporters.
‘That’s what we are pleased about because maybe six week ago we don’t find that winning goal, maybe we are still in the victim mode.
‘We showed the resilience you need to, you have to be able to win games in different ways. Now we are starting to win games from going behind.’
Referee Bramall endured a poor Fratton Park afternoon, irrespective of the penalty decision.
Even when Pompey fans were celebrating their late 2-1 victory at the final whistle, they managed to focus anger on the match official as he left the pitch.
At half time, Cowley sought to keep his players away from Bramall, although fired a few words in his direction as they left the pitch.
And the pair also exchanged pleasantries inside during the interval.
Cowley added: ‘We spoke at half time, only in a polite way, he gave what he saw.
‘It wasn’t so much the penalty, the foul count was so significantly against us in a game we were on top on until the penalty.’
A message from the Editor, Mark Waldron
You can support our local team of expert Pompey writers by subscribing here for all the latest news from Fratton Park for 14p a day.