The striker, who impressed against Tottenham at the weekend, had to be withdrawn after just 11 minutes with suspected damage to his knee ligaments.
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"The bad news is the injury," Mourinho told reporters in Romania. "It's a pity for the guy because, physically, he was in a very good moment.
"He played fantastically against Tottenham and deserved to start this game. So it's a pity but that's football."
"The doctor is very confident it is not a big injury like we had with Marco van Ginkel but it's something with his knee, his ligaments and we have to wait for the scans.
"Fernando knows that he doesn't play against Norwich on Sunday and will not go to join the (Spanish) national team."
Mourinho added that he was hoping Torres - who is banned for the visit of Norwich City this weekend after picking up two yellow cards against Spurs - would return against Cardiff City in just over two weeks' time.
"He knows that he has 15 days until the next match he can play, against Cardiff," the Portuguese said.
"If the injury is for 15 days I think he'll be fine."