The Blues had opened the scoring at Stamford Bridge through ex-Atleti star Fernando Torres in the 36th minute before Adrian Lopez responded for the visitors on the stroke of half-time.
Chelsea then conceded a penalty just prior to the hour-mark, which was converted by Diego Costa, and Mourinho feels that killed the contest before Arda Turan wrapped up proceedings in the 72nd minute.
"I think until the penalty they were not the best team," he told Sky Sports.
"We had the game, we had more possession, more chances, we scored a great goal - we conceded a poor goal - we knew at set-pieces we would have chances."
Just moments before the penalty, Chelsea had a fantastic opportunity to edge in front but Thibaut Courtois brilliantly denied John Terry's header which was a massive turning point according to Mourinho.
"Terry had a great chance but it was a fantastic save and after that the penalty killed the game and there was only one team in it. We were trying and the players were trying everything but from that the moment the reality is that we knew we were out," he added.
"Semi-finals and important matches are made of details and this was a big detail with the save and then the penalty that left them in a great condition. But congratulations to them they are a very good side and what they are doing in the Spanish league is fantastic and I congratulate them."
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