Claudio Marchisio opened the scoring in Manaus before Daniel Sturridge, fed by Rooney’s cross from the left wing, equalised two minutes later, though Mario Balotelli’s second-half header wrapped up the points for Cesare Prandelli’s side.
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“I don’t think it is the best position for Wayne,” Mourinho told Eurosport.
“But I think many, many times players must do sacrifices for their team and I think Wayne did well.
“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, Sterling and 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.”
England face Uruguay, who lost 3-1 to Costa Rica, in their second Group D fixture on Thursday and Mourinho feels Hodgson’s men can take positives from their defeat.
“England played very, very well,” said Mourinho.
“I don’t remember seeing England play so well in an important competition like the World Cup.
“In the next match against Uruguay it is forbidden to lose. In my opinion the English team had a very, very good positive game [against Italy].”