Jose Mourinho was denied a reunion with former club Real Madrid as Atletico Madrid inflcited upin Chelsea their heaviest European home defeat to book an all-Spanish Champions League final in Lisbon.
Fernando Torres had opened the scoring against his former club but the goal would only work as a false dawn for the Blues.
Adrian Lopez equalised on the stroke of half-time, before Diego Costa's penalty and Arda Turan's third saw Diego Simeone's side set up the first European Cup final between two sides from the same city against La Liga rivals Real.
With the carrot of facing former club Real in the first time since leaving the club last summer, Mourinho again opted for caution as Cesar Azpilicueta and David Luiz began in midfield behind an attack spearheaded by Fernando Torres and Eden Hazard, who returned from a three week absence.
Opposite number Diego Simeone made only one alteration from the goalless first leg draw, with Raul Garcia replaced by Adrian as the La Liga leaders looked to reach a first Champions League final since 1974.
Both sides showed a greater attacking intent from the off in contrast to the first leg and David Luiz was unfortunate not to see his overhead kick bounce into the corner after leaving Thibaut Courtois motionless.
Though the Chelsea back four had kept striker Costa largely quiet during the early opening, the Spaniard suddenly sprung into action and twice had shots from an angle blocked, Gary Cahill making the second diving challenge.
However, a defensive error at the other end was followed by Chelsea taking the lead in dramatic fashion at the other as Willian kept the ball in the corner, fed Azpilicueta and when the Spaniard's cross found the onrushing Torres the former Atletico striker benefitted from a deflection to wrong-foot Courtois.
The £50m man decided against celebrating out of respect for the club he supported as a boy but he would live to regret the decision not to saviour the moment as Atletico staged a turnround either side of half time.
Atletico equalised though Adrian's skewed finish after Juanfran's cross, before two-second half goals consigned Chelsea to another semi-final exit under Mourinho's guidance.
Samuel Eto'o returned from injury to bolster the Chelsea attack but his first involvement came at the wrong end as he tripped Costa and forced referee Nicola Rizzoli into awarding a penalty.
Costa converted with aplomb to give Atletico the lead on the night and in the tie and they sealed their place in the final in Lisbon next month as Turan reacted quickest to his own header which hit the bar, to calmly slot past a helpless Schwarzer.