Rooney, 27, received a good reception from the United fans before kick-off and Mourinho suggested he would not be surprised if such support changed the player's mind.
He said: "The most important thing is that he played very well. He was a real professional.
"He played for his club, played for the club that pays him, tried to win, tried to score. He was fantastic.
"After that, if he wants to leave, he has to say - or he decides now that he doesn't want to leave anymore.
"But I praise him. He played a fantastic match in these difficult circumstances.
"Many players in this situation can't express themselves on the pitch. They don't feel enough confidence or they cannot forget what is behind (them)."
Specifically on the crowd, Mourinho said: "In other countries it wouldn't be possible, in other clubs it wouldn't be possible.
"It doesn't matter the player you are, they don't want you.
"But they gave him fantastic support, it was good, it was nice - very English."
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