Pep Guardiola's Bayern Munich twice came from behind to beat Mourinho's 10-man Chelsea in Prague, winning the trophy with a 5-4 penalty shoot-out success after substitute Romelu Lukaku saw his effort saved by Manuel Neuer.
Mourinho felt aggrieved by the dismissal of Ramires for a second yellow card, a decision which left the Blues to play the whole of extra time with 10 men.
Mourinho made his feelings about referee Jonas Eriksson clear on the pitch and it continued afterwards as the self-proclaimed Special One reeled off a series of past instances where he felt hard done by.
"At Chelsea (in his first spell), I played two or three times with 10 men against Barcelona," he said. "I went to Inter and played a Champions League semi-final, one hour, with 10 men against Barcelona.
"I go to Real Madrid, I played again a Champions League semi-final with 10 men. I came back to Chelsea and played a Super Cup final with 10 men again.
"Go to analyse the actions and make your conclusions.
"I'm unlucky. Just that."
Ramires received his second booking for a foul on Mario Gotze.
Mourinho believes Eriksson should have been more lenient.
"If you are in love with football, you don't kill a final with a second yellow card like this," Mourinho said.
"There were many other yellow cards during the match that the referee didn't give.
"If you ask me in pure terms, rule by rule, yes it was a second yellow card. But you don't do every action in that way."
Chelsea thought they had handed Mourinho a first trophy of his second spell as boss when Eden Hazard netted in extra-time after Franck Ribery had cancelled out Fernando Torres' opener.
But Javi Martinez tucked in with the final kick of an astonishing game, forcing penalties.
The 2012 European Cup final between the sides had been decided on spot-kicks in Chelsea's favour and on this occasion, shooting towards the boisterous Bayern end, Lukaku's soft kick handed victory to the Germans.
"I'm disappointed," Mourinho added.
"In my opinion the best team lost. The team that deserved to win more lost. But that happens in football."
There had also been personal pride at stake for former Inter Milan and Real Madrid boss Mourinho, who had won three of his 15 encounters with Guardiola's Barcelona.
The Spaniard remains his nemesis and, not surprisingly, had a contrasting view of the enthralling encounter.
"It's his opinion," said Guardiola, when informed of Mourinho's thought that the best team lost.
"I have too my opinion. We have played unbelievably good football. The best team won. We had so many opportunities to score."
Guardiola declined to wade into the debate over Ramires' dismissal, the second booking coming for a challenge on Mario Gotze.
"I never speak about referees," he said.