Beaten at his own counter-attacking game by Argentine counterpart Diego Simeone, Mourinho's blue wall buckled then crumbled under the weight of Atletico power and precision in a superbly crafted 3-1 win at Stamford Bridge on Wednesday.
The Champions League semi-final defeat could be put down to Chelsea's inability to get an away goal in last week's 0-0 stalemate in Spain, but while Europe looks forward to a Madrid derby on May 24, Mourinho was left to rue his tactical choices.
Mourinho, who famously called himself "The Special One" when he first arrived at Chelsea a decade ago, was mockingly dubbed "The Semi-Final One" by Spanish newspaper Marca after a fourth successive failure at this stage of the competition.
He had the good grace to congratulate "a very good" Atletico team but missing out on a dream final against the club he left so acrimoniously last season, at the home of Benfica, where he briefly coached at the start of his career, represents a rare failure for a man adept at seizing opportunities.
He was ultimately found wanting because his own defensive "park the bus" tactics reversed him into a corner there was no driving away from.
His ultra-cautious approach to the first leg last week meant Chelsea came home without an away goal - and even when they took the lead on Wednesday through former Atletico favourite Fernando Torres, it was of no real significance to the tie.
Although Torres' strike put them ahead on aggregate, the fragile advantage was swiftly eradicated when Atletico capitalised on some slack Chelsea defending to equalise a minute before halftime through Adrian Lopez.
That goal put Atletico ahead on the away goals rule and they never looked back with Diego Costa adding a 60th minute penalty and Arda Turan sealing victory with a tap-in after his header rebounded back to him off the woodwork 18 minutes from the end.
Mourinho named six defenders in his 4-2-3-1 starting lineup with Torres the lone striker, and did not bring on attacking reinforcements Samuel Eto'o, Demba Ba and then Andre Schurrle until the second half.
Often heralded as a master tactician, the 51-year-old had appeared to have got it right once again - until Atletico equalised.
Mourinho could not be faulted for the series of rapid-fire defensive miscalculations that allowed Atletico to pull level so quickly but once they had, Chelsea were unable to find a way through the opposition defence again.
Simeone set his side up to defend deeply with two rigid banks of four when Chelsea came forward and they were better on the counter than the hosts as Turan worked tirelessly on the right while Koke and Costa made incisive runs when Atletico broke.
The key problem was that Torres was more or less operating by himself up front and apart from the goal, the Spanish forward contributed little to Chelsea's cause.
What Mourinho might have done better was to increase his attacking options far earlier than he did.
Although Eto'o replaced Ashley Cole after 53 minutes, Ba was a straight replacement for Torres after 67 minutes when Chelsea were already 2-1 down, and Schurrle only came on 13 minutes from time when the tie was effectively over.
Eden Hazard, Chelsea's 23-year-old Belgian international playmaker even seemed to question Mourinho's tactics afterwards.
He was quoted as saying on French TV station beIN SPORTS that Chelsea "were not made to play football."
Hazard, returning to the side after missing four matches through a calf injury, did not have his usual impact on the match apart from a few good runs in the first half.
Speaking afterwards he said: "Chelsea are not made to play football, we are good on the counter-attack, a bit like Real Madrid against Bayern Munich.
"Often I am asked to do it all by myself and its not easy."
Particularly frustrating for Chelsea was that the man who blocked their path to goal was one of their own players, the goalkeeper Thibaut Courtois, who has never played for his parent club but been on loan at Atletico for three seasons.
Mourinho said the turning point in the match came after 60 minutes when the 21-year-old Belgian made "an impossible save" to stop John Terry's header, and a minute later Atletico took the lead through Costa's spotkick.
One positive for Chelsea is that they have seen first hand how good Courtois is with the Belgian likely to be back at Stamford Bridge next season, challenging incumbent number one keeper Petr Cech all the way for his jersey.
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- Diego Simeone
- Fernando Torres