The Red Devils boss criticised the Belgium-born Brazilian for not staying and fighting for a first-team place at Old Trafford after opting for a season-long switch to the La Liga side earlier in the season.
Pereira's decision resulted in Mourinho questioning whether the midfielder had "the fight" to make it at United, even though he signed a new deal until 2019 just before leaving for the Mestalla Stadium.
"For sure, [Mourinho] is happy because Marcelino [Garcia Toral] is a very, very good coach as well and we are doing great," 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."
Pereira has played 17 league games for Valencia, who sit third in the standings and are in the semi-finals of the Copa del Rey.