An enthralling encounter was overshadowed somewhat as Mourinho berated officials, hinted his belief that there is a conspiracy against him and said the best team lost.
Pep Guardiola appears to have that effect on Mourinho, who has three wins from 16 games against his Spanish nemesis following the 5-4 penalty shootout defeat to European champions Bayern on Friday night.
It was the self-proclaimed Special One's first loss of his second spell as Blues boss and it was by the narrowest of margins.
The contest finished 2-2 at the end of extra-time, which Chelsea played with 10 men following Ramires' dismissal, as Javi Martinez netted with the last kick of the match.
Then, after nine successful penalties, Romelu Lukaku saw his effort saved by Manuel Neuer, handing Bayern victory.
A more measured Mourinho opinion was that his team, which beat Bayern to lift the 2012 European Cup, showed their outstanding potential.
"All of us we will go (home) disappointed, but at the same time we go with the notion that we will have a better team," Mourinho told Chelsea TV.
"To play against the champions of Europe the way we did, with 11 (men), with 10, and we deserved to win. The boys deserved to win. They did everything.
"We got the feeling of the team we are building, the character we are building, the personality we are building.