Courtois played the full 90 minutes against the Spanish side with Petr Cech being left on the bench, but Mourinho has claimed that his decision was based on giving the Belgian stopper a chance to improve his match sharpness after missing the majority of pre-season.
The 51-year-old told the club's official website: "I played Thibaut for 90 minutes because he was injured and didn't play last weekend.
"Petr played two matches in Turkey and the first half against Ferencvaros. Since he arrived, Courtois has only played 45 minutes against Werder Bremen. He needs to play.
"The fact that Courtois played 90 minutes wasn't me saying that he's first choice for Monday, it's because he didn't play the last three matches. The players don't know who is first choice yet. When will I tell them? On Sunday."
Cech has made 470 appearances for Chelsea since signing for the club in 2004, while Courtois has recently returned to Stamford Bridge after three years on loan with Atletico Madrid.