Courtois is currently on loan at Atletico from Chelsea and was initially not expected to face his parent club due to a clause in his contract.
However, UEFA intervened in the situation and warned Chelsea that it was against the competition rules to have an influence over another team's selection, meaning that 21-year-old Belgian is now free to play.
"I think that on UEFA decisions it's better not to comment, you just accept or if you don't accept you don't make any comment. UEFA decides and I think managers don't comment," Mourinho told reporters.
Courtois has been linked with a move back to Chelsea this summer as a replacement for the ageing Petr Cech, but Mourinho once again refused to comment on the speculation.
"I don't speak about players from other teams," he added.
Chelsea travel to the Vicente Calderon for the first leg of the semi-final tomorrow night before the return fixture at Stamford Bridge next Wednesday.