Pereira spent last season on a season-long loan at Granada and impressed for the Spanish side despite their relegation.
The Brazilian returned to Manchester United in the summer and was hopeful of pushing for a place in the first-team.
But he was left out of the matchday squads in the opening weeks of the season and with the transfer deadline approaching pushed to leave.
Pereira eventually returned to Spain but this time joined Valencia which left Mourinho irate.
Mourinho said: “It was a personal decision that I don’t agree with, a decision I don’t think honestly is the best decision for him, a decision that disappoints me.
“You have to be ready to fight for the position and I am disappointed he left.
“But was his decision, I opened the door, he has a long-term contract, we have the option to bring him back on Jan. 1, so is not a drama but is a decision which disappoints me a little bit.”
But Pereira insists he made the decision to leave for the benefit of his career.
“That’s why it is difficult,” Pereira told The Guardian.
“He told me I had to stay but I wanted to play and get more minutes.
“He wanted me to stay there and it was important [to him], but I needed to do this.
“This was important for me and my career. And I’m sure if it works out, next year I will be back there and it will be better for both of us.
“In the end I think he is happy because he is a very honest coach.
“I was talking to him right up to the very last minute when I came here.”