Ligue 1 champions PSG progressed to the quarter-finals on the away goals rule after drawing 2-2 after extra-time at Stamford Bridge, despite being down to 10 men in the 31st minute when Sweden international Ibrahimovic was dismissed for a sliding challenge on Oscar.
The decision of referee Bjorn Kuipers looked a harsh one with Ibrahimovic appearing to pull out of the challenge.
And Mourinho, who worked with Ibrahimovic during his time as Inter coach, believes it would be a shame if the former Barcelona striker was not allowed to play in the quarter-finals.
"I was very far from the Ibrahimovic situation and I couldn't see it," he said. "I spoke with him after the game, and when he speaks with me he's always honest.
"He would tell me if there was a reason for a red card. He was very disappointed. If that's the case I hope they can minimise the mistake and let him play in the quarter-finals because if he did nothing wrong he deserves that."
However, the Portuguese stated that Ibrahimovic's punishment should be passed on to to former Chelsea man David Luiz - who scored PSG's first equaliser - for an apparent elbow on Diego Costa that went unpunished on the night.
Mourinho was also less than impressed that Costa was denied a first-half penalty after going to ground under a challenge from Edinson Cavani.
"It was a clear penalty on Diego Costa. Once more I think it's a waste of time and money to have officials behind the goal because normally they do nothing," he added.
"If he cannot see a penalty 10 metres from him where it's completely clear it's a waste of time and money.
"David's elbow I didn't see, but when UEFA gives him the man of the match I have to believe there was no elbow because I can't believe UEFA would give the man of the match to someone who made an aggression.
"Because they cannot give us the penalty, maybe they can do what is fair from the disciplinarian point of view and suspend David and take the red card off Ibra and let him play in the quarter-finals."
