The 28-year-old has been widely criticised for his display on the left flank for Roy Hodgson's side as he failed to have a major impact on the game.
However, the Portuguese feels that Rooney played well despite not being in his best position through the middle.
Mourinho is quoted as saying by The Mirror: "I don't think it's Wayne's best position, but many times players have to make sacrifices for the team and I think he did well.
"In the moment of defeat it is normal to try and find reasons for the defeat, but it is fair to say the reason for England losing was a great team."
England are next in action against Uruguay on Thursday in a must-win game for Hodgson's side.