Atletico equalised just before half-time and Belgium goalkeeper Thibault Courtois, on loan from Chelsea, showed lightning reactions to keep out a John Terry header on the hour.
Less than a minute later Chelsea striker Samuel Eto'o brought down Diego Costa in the area and the Atletico forward converted the subsequent penalty.
"The difference was one minute in the second half where a goalkeeper makes an impossible save and instead of 2-1 for Chelsea there was a penalty...and after that it was 2-1 for Atletico. And that completely changed the game," Chelsea's Portuguese coach said.
Mourinho, who won the Champions League with Porto and Inter Milan, suffered three successive semi-final defeats with Real Madrid before rejoining Chelsea at the start of the season.
In his first spell as Chelsea coach from 2004 to 2007 he took them to the semi-finals twice and lost on both occasions.
"These matches are normally decided by details and that minute had two details - the save was amazing - and the penalty," Mourinho said.
"I think that minute was crucial - after that Atletico had complete control. We had the feeling that the game was lost, they had for sure the feeling of much more confidence. They played very well - a very mature performance and I congratulate them," he added.
Mourinho felt the difference between his side and Atletico was that Diego Simeone had been building the Spanish league leaders for three years and he had been back at Chelsea only one season.
"It's the difference between one year and three and it's a big difference...they are a very good side, very adapted to the ideas of this manager every player fits his idea of how to play," he said.
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