The Spanish side cruised into the competition's quarter-finals with a 5-2 aggregate victory following a 1-1 stalemate in the Russian capital last month.
Kaka was the man of the match at the Santiago Bernabeu, assisting Gonzalo Higuain for the first goal and being heavily involved in the team's attacking plays before being replaced in the 75th minute.
"He had a spectacular match," Mourinho told reporters in the press conference after the game. "He had his best games at AC Milan, but he has never worked harder than now.
"He does fantastic work for the team and it is normal that he does not have enough strength in his legs after 75 minutes.
"We created our best chances in the first half."
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Mourinho then played down the fact that he will be unable to count on Xabi Alonso in the first leg of the quarter-finals, as the Spanish midfielder will have to serve a one-match suspension after being booked on Wednesday.
"There is no reason to cry because Xabi will not be able to play," he added.
"We are fine in the midfield: [Estaban] Granero and Lass [Diarra] can easily play with [Sami] Khedira and Nuri [Sahin], whose spirits we're trying to raise. Alonso will rest and will be able to play all league games. He will be fit to the end."
The Portuguese coach went on to praise Madrid's display against CSKA, saying that his side deserved to win the match.
"Although CSKA had a good chance to score at the beginning, we controlled the match," Mourinho explained.
"As soon as we lost the ball, we put pressure on them and we controlled proceedings.
"This was not a spectacular match, but it was one of great maturity. After we were up 3-0, we stopped working at the same level."
Quizzed on his preferred opponent for the quarter-finals, Mourinho said: "I am not thinking about that. The most important thing is that we are through and now we have to wait.
"Some great teams are not in the quarter-finals such as Manchester United, City, Arsenal, Inter and Valencia. There have been some surprises and that's good for football. Everybody thinks the final should be Real Madrid-Barcelona, but I disagree."
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