Thibaut Courtois dived low to his left to keep out a John Terry header when the score in their second leg was 1-1.
Moments later, striker Diego Costa won and scored a penalty to put Atletico ahead before Arda Turan added a third.
"One minute in the second half decided everything," said Mourinho.
"A minute where the Atletico goalkeeper
makes an impossible save to a John Terry header then the penalty that
kills the game.
"After that there was only one team with morale high, knowing with half an hour left they had control.
"For about 60 minutes, we had the game, but semi-finals and important matches are made of details and this was a very important detail.
"Congratulations to them because they are a very good side and what they are doing in the Spanish league is fantastic."
Belgium international Courtois, 21, was making his 150th appearance for Atletico in his third consecutive season on loan from Chelsea, for whom he has never played.
He has helped the capital side to their first European Cup final in 40 years and to the top of the Spanish league with three games remaining.
Having been cleared to play against his parent club by Uefa, he kept a clean sheet in the 0-0 first leg and foiled both Terry and David Luiz at Stamford Bridge.
When asked whether he would keep Courtois at Stamford Bridge next season, Mourinho simply said the 21-year-old was "an Atletico player".
The result was Mourinho's fourth successive Champions League semi-final loss following defeats at the same stage in all three of his seasons at Real Madrid, the club Atletico will face in the final.
Despite defensive errors contributing to all three goals, the Chelsea manager absolved his players of blame.
"I can't be critical with a group of players that from day one is giving everything, trying everything," he said.
"With problems with injuries, suspensions, with players that cannot play in the Champions League, I'm proud of them.
"Obviously it's disappointing to lose a semi-final second leg, especially at home, but I am proud of them. I prefer to say we did everything that was possible for us.
"We tried with honour and professionalism and we gave everything, but Atletico were mature and professional and they were in complete control."
Mourinho insisted his team, who still have an outside chance of winning the Premier League title, would come back stronger next season.
"Next season will be better than this season - that's our objective," he said. "Our young players will be better, hopefully we will have a couple of players to improve our team and we will try to do better."
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