The Spain international has been left out of Mourinho's starting XIs so far this season despite being a regular under Rafael Benitez, leading to speculation linking him with a move away from the club, with Arsenal reportedly interested.
Mourinho told reporters: "He didn't play against Man United, it was my option. I have always reasons for the options. I feel that it's my duty to explain to the players the reasons for my options - and I do.
"I don't feel it's my duty to explain to the media the reason for my options. I don't always do [it]. Everything is clear between me and the player. We have no problems.
"I think he's a very important player for us. He wants to be a very important player for us. He wants to stay. I want him to stay, the club want him to stay. There is no story."
Chelsea face Bayern Munich in the European Super Cup on Friday.