Mourinho’s Madrid side looked to be on course for a European showdown with Chelsea after Cristiano Ronaldo put Los Blancos 2-0 up on the night and 3-2 ahead on aggregate.
But Arjen Robben tucked away his penalty before the break to level the tie and Bayern eventually triumphed after extra-time and a dramatic shoot-out.
And Mourinho, who led Chelsea to two Premier League titles, an FA Cup and two League Cups during his three-year spell at Stamford Bridge, said he will be backing the Londoners in the final in Munich on 19 May.
“John [Terry] is missing but Chelsea are there [in the final] and that is the most important thing,” said Mourinho.
“I just hope it is a good final and of course I want the Blues to win, even though I have a lot of respect for the reds. I have a blue rib, still. Inter and Chelsea mean a lot to me.
“I think Chelsea’s boys were heroes [against Barcelona], absolute heroes. Some people think they are the masters of the game and they will criticise Chelsea in the same way that they criticised Inter two years ago, but they know nothing. Nothing.
“They know nothing about character and personality. They know nothing about the effort or what it is to resist physically, emotionally and technically, with 10 men. They know nothing about organisation. They know nothing.
“That’s why my heroes at Chelsea are in my mind and why Chelsea deserve to be in the final. One of the great things about football is that it is unpredictable. Chelsea have fantastic fans and so do Bayern Munich so I hope they enjoy the final. And I hope Chelsea win.”
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