Morata was taken off after Sergio Ramos was sent off when Real were 2-0 up.
Morata said that the most important thing was that the team won and that he is "in no rush" to play every minute.
"There are times when things like this happen," Morata told the club's official website. "That's how it goes but I'm happy because the team won.
"Mourinho told me this is what it is and I accept that. For me it is a great pride to be part of the team. I am learning from the best in the world and there is no rush.
"We were doing well due to our two early goals. Afterwards we knew that it was going to be difficult with one man less. With ten men, it takes a lot to win."
Real are third in La Liga, 16 points behind Barcelona.