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.
"Everybody gave everything. Everybody was fantastic. Everybody gave heart, everybody gave soul.
"I'm very happy with the boys, but, of course, disappointed for them."
Twice Bayern recovered from behind after Chelsea went ahead through fine strikes from Fernando Torres and Eden Hazard, who both performed strongly.
Petr Cech made a series of outstanding saves, Ashley Cole kept former Blue Arjen Robben quiet, the 35-year-old Frank Lampard was influential in midfield.
The men around him performed well under wave after wave of German attacks, led by newly-crowned European player of the year Franck Ribery, who scored Bayern's first equaliser.
Chelsea defender Gary Cahill said: "The way they got forward was frightening at times with the overlapping runners, Robben and Ribery on the wings.
"At times it felt like the Champions League final (in 2012). I thought we defended well as a team, the spirit was there and we were just seconds away from winning.
"We did well but football is cruel at times. We dug in hard, especially in extra-time. I thought we did enough."
Cech also made reference to the 2012 European Cup final, when a rearguard action from Chelsea earned victory, on penalties, on Bayern's own ground.
"It was a great match," Cech said.
"It is a shame we did not come out with a better result. It's always hard if you concede in the last minute, but football is like that sometimes.
"Two years ago it ended up with the opposite result."
After suffering the ignominy of becoming the first holders to exit the Champions League at the group stages last term before responding to win the Europa League, Cech is confident of a stronger display this season. The Blues have been drawn against Steaua Bucharest, Basle and Schalke.
"I think we showed that we are ready to compete with everybody," he said.
"This Bayern team are the Champions League winners and they won the treble last season, so they were the favourites in this match and for this Champions League campaign we showed that we are ready to compete."
While undoubtedly promising for a Chelsea side who have Samuel Eto'o and Willian to bolster the ranks, the contest showed the Blues have work to do, too.
There are now two weeks to reflect on the defeat, with a trip to Everton in the Barclays Premier League awaiting Chelsea following the international break.
Lampard, Chelsea captain on the night, like Mourinho is optimistic for the campaign ahead.
"We need to take the positives out of this game and can be proud of our performance with 10 men," Lampard said.
"We played against a team considered as the new force in world football and we showed that we have a lot to offer."