Diego Costa killed Arsene Wenger's last hope of a glorious Arsenal farewell as his goal sent Atletico Madrid through to the Europa League final.
In the final, Atletico will meet Marseille who scored a 3-2 aggregate victory over hosts Salzburg.
Wenger's 250th European fixture with Arsenal also proved to be his last, decided by a typically ruthless finish from Costa, who delivered the sort of barnstorming display defenders must have nightmares about.
Arsenal's defence, fragile and nervous throughout, were particularly susceptible and this 1-0 defeat, 2-1 on aggregate, means Wenger's final season in charge will end with his team missing out on Champions League qualification for a second year in a row.
For all his domestic achievements, Wenger will also depart without a European trophy to his name and it remains to be seen how sitting outside the continent's premier tournament will affect Arsenal's pursuit of a new coach, and players, this summer.
"I'm very sad tonight," Wenger said. "Unfortunately you have to go through that - the game can be very cruel, sometimes very nice, but the suffering is very strong tonight."
More immediately, there was the concerning sight of Laurent Koscielny being carried off on a stretcher in the 12th minute after the defender went down, with nobody near him, clutching his left Achilles.
"It doesn't look very good, it's his Achilles," Wenger said.
"You can always hope for a miracle in the scan but if he has a ruptured Achilles, his chances for the World Cup are non-existent."
Koscielny's exit made a tough task all the more difficult for Arsenal, who were always going to be up against it at the Wanda Metropolitano, where Atletico have not lost in the league all season and not conceded a goal since January.
It was perhaps also telling that Costa's physicality and Atletico's defensive rigour ultimately proved decisive, two qualities Wenger's Arsenal in recent years have so lacked.
"Costa came back here for nights like this," Atletico coach Diego Simeone said.
"To be important, to lead from the front. This side needs an aggressive striker and that's exactly what he is."
Ronaldo stars
Marseille booked final meeting with Atletico after Portuguese defender Rolando struck in extra time to grab a 3-2 aggregate victory in Salzburg.
Salzburg produced a rousing second-half performance to wipe out a 2-0 first-leg deficit, but Marseille became the first French side to reach a European final since 2004 despite a 2-1 defeat on the night.
Amadou Haidara gave the dominant hosts hope early in the second half with an excellent individual effort before Bouna Sarr's own goal levelled the semifinal.
Rudi Garcia's visitors survived some late scares to force a further half-hour and substitute Rolando volleyed home a 116th-minute Dimitri Payet corner that shouldn't have been given.
The 20-year-old Haidara, the outstanding player on the night, was sent off as his frustrations boiled over, as Salzburg's incredible run which included wins over Borussia Dortmund and Lazio came to an end.
Marseille, runners-up to Valencia in the UEFA Cup 14 years ago, will make the short trip from their Stade Velodrome home to take on Atletico in the final in Lyon on May 16.