"I think there was a Wayne before the Slovakia-England and a Wayne after the Slovakia-England," Mourinho said.
England won 1-0 in Trnava but Rooney did not impress in a midfield role.
Mourinho added: "I am not blaming Sam (Allardyce, England manager), not at all.
"I am blaming the people that after England-Slovakia were, in my opinion, too strong with somebody that is a very important player in the history of English football.
"I think it was too much but I still think, a big boy like he is, he has to face it in a strong way."
Mourinho also insisted his captain is not too important to be dropped from the starting XI.
" In football everyone is the same and if he has to go on the bench, he goes on the bench. If he has to stay at home, he stays at home," he said.
"But that doesn`t mean that you don`t trust him or you have a problem. Not at all.
"We have no problems. He is our captain but, of course, no privilege - he is like anyone else."
