The Manchester United forward provided the assist for Daniel Sturridge's first-half goal, but was deployed in a wide position for much of the second period.
Mourinho has said that Rooney's workmanlike mentality makes him effective in those positions, but has claimed that the best part of the 28-year-old's game is sacrificed in wide areas.
"I don't think it is the best position for Wayne. But I think many, many times players must do sacrifices for their team and I think Wayne did well," Mourinho told Eurosport.
"I think in this moment after defeat it is quite easy and it is a normal tendency to try and find the reasons for the defeat but I think it is fair to say that the reason for the England defeat was a great Italy.
"Obviously Roy was trying to play at the same time Rooney, [Raheem] Sterling and [Danny] Welbeck with Sturridge, and to do that somebody has to play a bit more on the side and Wayne did his job. He got an assist for the goal with good participation in the game. But he loses a bit of his danger because he is naturally a goalscorer when he plays more in central positions."
Mario Balotelli scored the winner for Italy.