The Blues failed to record a shot on target during a disappointing performance that ended with a 1-0 defeat, and Mourinho has admitted that he saw fatigue in some of his players during their loss in Switzerland.
The 50-year-old told the club's official website: "Maybe I could make more changes from the game on Saturday for today, but when the players play so well, there's a big temptation to keep the team and the players that played so well.
"I spoke with all of them individually and of course, all of them told me that they were perfect to play.
"Some were so-so but others were really in trouble today. I could see many signs of fatigue, but I don't want to take the credit away from the opponent because they were better than us."
Despite the setback, Chelsea have qualified for the Champions League knockout stages with a game to spare.