Mourinho's Real lost a penalty shootout against Bayern Munich, meaning the Germans will face Robert Di Matteo's men in their own Allianz Arena.
Mourinho said: "Chelsea mean a lot in my life and I would like them to win the final. John Terry is missing, but Chelsea is there, which is the most important thing. Of course I want the Blues to win, but I have respect for the Reds of Munich."
In a sideswipe at arch rivals Barcelona, he added: "The Chelsea boys were heroes yesterday, absolute heroes. I know some people think Barcelona are the masters of the game and will criticise Chelsea like they criticised Inter Milan two years ago. But they know nothing about character, about effort, about a team with 10 men resisting tactically, physically, everything.
"That's why I have in mind the heroes of Inter and the heroes of Chelsea in this match."