The Swedish striker appeared to become riled as he challenged with two Valencia players and went over the ball in a challenge with Andres Guardado, prompting referee Paolo Tagliavento to brandish the red card.
The dismissal came swiftly after Valencia pulled a goal back in stoppage time, having trailed 2-0, and the Spanish side will head to Paris in three weeks' time looking to make up a 2-1 deficit, with Ibrahimovic suspended.
Leonardo was asked if he regretted the late twist to the night's events.
"To concede a goal, that can happen due to fatigue for example," Leonardo said.
"But the red card... I think Ibrahimovic pays for his reputation. If it was another player committing this foul, he wouldn't be sent off.
"Suddenly, there is a slight bitter feeling because of it."
Carlo Ancelotti's Ligue 1 leaders had taken command at the Mestalla with first-half goals from Argentinian pair Ezequiel Lavezzi and Javier Pastore, with Valencia's late reply coming from Adil Rami.
"Even when you lead 2-0, it's not easy," Leonardo said.
The Brazilian former World Cup winner stressed it was worth remembering the progress PSG have made since Qatar Sports Investments took control of the club in 2011.
"It's only been a year and a half since QSI took over the club," he said, according to psg.fr.
"We are still in the construction phase. Our ambitions isn't only to win a match in the last 16 away from home. It's more than that.
"To win the Champions League? This year, I don't know. But after that..."
Manager Ancelotti agreed with Leonardo's assessment of Ibrahimovic's dismissal.
"It wasn't deserved," he said. "I don't under stand it, it isn't fair."
Italian Ancelotti added: "We played a good match on a difficult pitch. There was quality and a good attitude. We will need to have this same attitude in the return match.
"We had a lot of chances to score and we defended very well. It's a very good performance even if we let in this goal at the end of the match."
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