The sporting director felt the Sweden striker was handed his marching orders because of a pre-meditated view of his character on behalf of match officials
First-half goals from Ezequiel Lavezzi and Javier Pastore gave the Ligue 1 outfit a commanding lead at the Mestalla, but a late Adil Rami header for the hosts and the dismissal of the Swede gives los Che hope ahead of the second leg of their last 16 clash.
"Ibrahimovic's red card was a bit severe. It was because of his reputation," Leonardo told beIN Sport.
Parisiens' defender Mamadou Sakho was left disappointed at the conceding of such a late goal, but insisted his side could still be happy with their night's work.
He added: "We are really disappointed to concede a goal like that, especially right at the end of the game.
"But, overall, it is a good result for us to come here and here win."
Valencia midfielder Tino Costa, who claimed before the game that his side would win on Tuesday night, remained philosophical in the aftermath of the loss.
"As we all know, in football anything can happen and with that goal at the end the atmosphere in our dressing room is that bit better."