The Italian boss was unhappy after the full-time whistle at Estadio Mestalla, despite watching his side emerge with a vital victory.
Goals from Ezequiel Lavezzi and Javier Pastore had put the visitors in a commanding lead, but a stoppage-time strike from Adil Rami and the dismissal of the Sweden striker gives the Spanish side hope ahead of the second leg.
"Ibrahimovic's red card was not deserved. I don't understand it. It's unfair," Ancelotti told Canal+. "We conceded a goal and Ibrahimovic got a red card, and I don't think that he deserved it because it was a normal tackle. And so, because of this, we are really disappointed because the play was really good, we played really well, focused on the game, and for this we have to be happy but the end of the game was not good for us.
"I think it was a normal tackle, nothing special, I was surprised to see a red card."
The Italian boss also admitted that his side could not afford to fall victim to complacency when Valencia visits Parc des Princes in the second leg of their Round of 16 tie.
"Valencia are a good team and we have to know that we have played just the first half of this game, and we have to play the second half at home," Ancelotti added. "It will be better for us, but we have to pay attention."
The Ligue 1 club's director, Leonardo, also gave his view on the late dismissal of Ibrahimovic and suggested the red card was as a result of a pre-meditated view of his character on behalf of officials.
"Ibrahimovic's red card was a bit severe," Leonardo told beIN Sport. "It was because of his reputation."