The Blues edged into an early first-half lead when Spanish striker Fernando Torres finished off a slick Chelsea move started by the impressive Eden Hazard.
However, despite the early setback, Bayern were largely dominant and newly-crowned Best Player in Europe Franck Ribery capped a good week with a brilliant equaliser in the 47th minute.
Ramires was dismissed for a second bookable offence with eight minutes of normal time remaining as the showpiece went into extra-time, with Hazard appearing to have scored the winner in the 93rd minute.
But Chelsea couldn’t contain Bayern as Dante netted a last-gasp strike which forced the match into a penalty shootout, with Blues youngster Romelu Lukaku missing the decisive spot-kick.
“Yes, I’m disappointed,” Mourinho told his post-match news conference.
“I’m disappointed because in my opinion – and it’s just my opinion which I can have without being punished – is the best team lost.
“The team that deserves to win more lost. But that’s football. Sometimes it happens. The best team doesn’t always win. It’s acceptable because that’s football.”
On Ramires’ sending off, Mourinho added: “Football is 11 against 11. 11 against 10 is of course easier for the team with 11 and the team with 10.
“I have a fantastic experience with playing with 10 men in Uefa matches. My players gave absolutely everything.”
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