A goalless first leg left the tie finely poised with a place in the May 24 Lisbon showpiece at stake against Mourinho's former club, who emphatically ended Bayern Munich's title defence on Tuesday night.
"Champions of Europe, we've done it before," sang the Stamford Bridge crowd as they urged the Blues on - and Fernando Torres gave Chelsea the lead against his former club.
But that was as good as it got for Mourinho's men, who found themselves level within eight minutes when Adrian netted before half-time for the Primera Division leaders.
Chelsea's task became all the harder due to the interventions of two players who could be playing for them next season.
Thibaut Courtois, playing against his parent club, saved a John Terry header before Diego Costa's penalty meant Chelsea required two goals to advance.
David Luiz hit the post with a header before Arda Turan turned in Atletico's third to send Atletico boss Diego Simeone delirious and running down the touchline in a manner reminiscent of Mourinho.
The Spanish side had won only one of nine previous fixtures away to English opposition - at Leicester in the 1997/98 UEFA Cup - but their second success extended their remarkable season.
It was Mourinho's fourth successive loss at the semi-final stage as the 2012 winners were eliminated and left to focus on their slim Premier League title hopes.
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