The Belgian appeared to be out cold when he collided with the knee of Alexis Sanchez midway through the first half at Stamford Bridge but, after treatment, was allowed to carry on.
Fifteen minutes later, with blood apparently coming from his ear, he was led off to be replaced by Petr Cech, who still wears a head guard after fracturing his skull in 2006.
Asked whether Courtois should have come off immediately, Mourinho said he had no say in the decision.
"I just get decisions. Does he stay or does he have to leave? I don't have the medical qualities to discuss," he said.
"They told me no, he couldn't continue. I was just worried for the kid, not worried about the game or the performance,” he added.
"I always tell (the medical team) that when I'm on the bench I don't want to communicate with them, I just want them to tell me a decision. It's correct they take control,” he further said.
The incident was similar to one involving Tottenham Hotspur keeper Hugo Lloris last season when he was allowed to play on after being knocked out in a collision with Everton striker Romelu Lukaku at White Hart Lane.
Tottenham were criticised for their handling of the Lloris incident with leading head injury organisations insisting that the decision as to whether to stay on the pitch should have been taken out of his hands by independent medical advisors.
Brain injury organisation Headway accused Tottenham at the time of an "irresponsible and cavalier attitude".
Having long-standing Chelsea first choice keeper Cech ready to come on underlined the depth of Chelsea's squad.
"We have two of the best three goalkeepers in the world," Mourinho said.

"When one is injured and comes off, and the other one comes on, no problem. There is no change in my heart. I was so confident Petr would once more do a fantastic job for us,” he added.
Courtois'sinjury could put the goalkeeper out of Belgium's European championship Group B qualifiers against Andorra on Friday and Bosnia on October 13.

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