In classic Mourinho-style, Roma drew 0-0 against Leverkusen at the BayArena to win 1-0 on aggregate.
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Edoardo Bove scored the pivotal goal back at the Stadio Olimpico last week while Xabi Alonso's side huffed and puffed but could not break down a resilient Roma defence.
And they were aided by some classic gamesmanship, principally by two ex-Manchester United stars in Nemanja Matic and Chris Smalling.
Deep into stoppage time, Serbian midfielder Matic hit the deck from an innocuous challenge and stayed down for a length of time.
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That infuriated the Leverkusen team, who even tried to haul the 34-year-old to his feet while Smalling intervened.
It led to Edmund Tapsoba getting a yellow card for his over-exuberant actions while a gleeful Mourinho was seen cheering on from the touchline.
The Portuguese coach was roaring in celebration as his side pulled out every trick in the book to secure passage to the Europa League final.
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Both Matic and Smalling he knows well from his time in charge of United, where they won the Europa League in 2017 while their expertise will be needed next month.
Full-time was blown minutes after the incident with Roma clinching victory to set up a finale against Sevilla next month at the Puskas Arena in Hungary.
It is a remarkable achievement for Mourinho, who helped the Italian side win the Europa Conference League last season in the first competition of its kind.
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Winning the Europa League would see the Giallorossi go a step further while it is the first time the club have reached the final since 1991, which they lost to Inter Milan.
"My concern isn't marking my place in the Roma history books," Mourinho insisted.
"It's helping these kids [players] to grow and achieve important things.
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"It's also helping the Roma fans who have given me so much since day one. It's an immense joy to get to another final."
Sevilla mounted a comeback in the second leg of their Europa League semi-final against Juventus to reach a seventh final.
After Dusan Vlahovic scored the opener, Suso equalised before Erik Lamela landed the winner in extra-time.
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Sevilla have become specialists in the competition, winning six Europa League titles in 2006, 2007, 2014, 2015, 2016 and 2020.