The Blues scored first but ended up losing the semi-final second leg by two goals at Stamford Bridge as Atleti set up an all-Madrid final with arch rivals Real.
Despite the defeat, Mourinho was complimentary towards his squad for overcoming plenty of setbacks during their Champions League journey which ended at the hands of Diego Simeone's vastly improved Los Rojiblancos.
"I can't be critical with the group of players who from day one tried everything," he told Sky Sports.
"We had problems with injuries and suspensions and players who can't play in Champions League and with difficult moments in the Premier League too this group have had difficult moments but I am proud of them.
"Obviously it is disappointing to lose the second leg of a semi-final, especially at home - but I can't criticise them for a mistake, we did everything possible for us.
"We never really had Atletico in a position where we had an advantage where they had to chase a game, maybe ten minutes, five minutes. But that is football and we have to accept that."
Fernando Torres netted against his former club in the 36th minute when he slotted beyond Thibaut Courtois but Atleti rallied on the stroke of half-time when Adrian Lopez was on hand to loop home his effort from Juanfran's volley across goal.
The contest was wrapped up just under 20 minutes from time when Arda Turan was left unmarked in the area, after his initial header had been tipped onto the crossbar by Schwarzer, with the deflection falling favourably for the Turkey international to side-foot home.
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