The defender was spotted visibly upset as he walked off after a substitute appearance in Thursday's 5-3 victory.
"Santon has always been called up, but he isn't calm enough right now. I am leaving him at home and it is my choice," explained Mourinho.
"Davide is not going through an easy time, aggravated by the fact that today on the front page of an important newspaper there were lies written about him. That doesn't help such a young player.
"I did not call him. I spoke to the lad for an hour in my office, face to face, along with my assistants who have worked with him for many years."