Departing coach Arsene Wenger’s side failed to score the one goal they needed to progress from this tense Europa League semi-final and keep their dream of returning to Europe’s elite alive, as they just fell short of staging an unlikely comeback.
Diego Costa’s winner on the night made no difference to the outcome as Arsenal’s inability to score was their undoing having conceded a late away goal in last week’s 1-1 first leg draw in London.
After masterminding two decades of Champions League football for Arsenal, Wenger will now depart this summer having failed to get his team to deliver for two successive seasons.
He always claimed it was a feat that should not be underestimated and how right he was.
Aside from the blow to Wenger’s pride, on his 250th time in charge of a European tie, and the disappointment of the club’s supporters it was a horrendous night here for captain Laurent Koscielny, who tore an Achilles early on and will now miss the World Cup too.
Arsenal gave everything, but ultimately the best team will go to the final in Lyon.
The omens were there from the kick off as the remarkable atmosphere generated by a 60,000 capacity crowd at the relatively new Madrid stadium seemed to make it hard for the Arsenal players to hear each other judging by an early misunderstanding at the back between Koscielny and keeper David Ospina.
If that betrayed Arsenal’s nerves then Costa, recalled after missing the first leg through injury, barged into Koscielny off the ball, setting the tone for their personal battle.
Aaron Ramsey and some sweet Mesut Ozil skills helped set up a dangerous attack which ended with Thomas Partey turning the ball just past his own post for a corner.
Costa, Arsenal’s nemesis from his time at Chelsea, was then clear on goal at the other end moments later, but could only shoot into the side netting under pressure from Ospina.
That was all inside the opening ten minutes, but then the match shuddered to a halt when Koscielny collapsed in agony, suffering a torn Achilles.
Costa, to his credit, was the first to signal the referee to stop play and call for treatment. And the 3,000 traveling fans were sportingly joined in sympathetic applause for the distraught French international defender when he was eventually carried off on a stretcher.
That will keep Koscielny out of the World Cup, possibly the start of next season, and is terrible luck for a player who was being nursed through the end of the season having been rested for five of the last six league games.
Calum Chambers, who came on as substitute, looked more comfortable at the back, though and Arsenal, with Jack Wilshere now captain, were the dominant side.
But that seemed to suit Madrid’s tactics, happy to let Arsenal have the ball so long as they had men in numbers behind the ball. They knew that even if they scored Arsenal’s target of having to score an away goal would remain unchanged.
Arsenal then had to endure a spell of pressure with Thomas Partey and Antoine Griezmann both going close to scoring.
Arsenal and Wilshere, in particular, began to look frustrated and the midfielder was the first player booked for a clattering into Atletico counterpart Gabi.
Then, in first half injury time Griezmann played in Costa, Mustafi went missing and the Spain forward easily shrugged off Hector Bellerin before waiting for Ospina to commit before lifting a left foot shot into the net.
The goal might not have changed Arsenal’s objective, but the timing and ease with which Madrid scored was enough to deflate the confidence of even career over-optimist Wenger.
Arsenal had played well, without creating clear cut chances, but had once again been outwitted by a more experienced side with an impenetrable defence.
Wenger would have to give the half-0time team talk of his life and the players to respond. Either way, they would need to improve and go for it.
When they did, Madrid were rock solid and ruthless, Gabi collecting a yellow card for a professional foul on Danny Welbeck as he attempted to launch a dangerous break away attack.
But when Ramsey found space in the area he could not get a shot off of any note.
And Arsenal were just as likely to concede, getting caught on the break, as they were to score now.
Arsenal continued to attack, though, as they had to and an attacking spell was punctuated by a Granit Xhaka shot which Jan Oblak tipped around a post for a corner.
Soon after Griezmann nearly added his second goal of the tie Wenger sent on Henrikh Mkhitaryan for a disappointed Wilshere with just over 20 minutes to go.
The Armenian made an impact but not a big enough one and Madrid saw out the danger without really bringing out one of Oblak’s trademark world class saves.
They blew it in the first leg they should have won at a canter and were left lying distraught on the pitch in failure when the final whistle went. Wenger made for his opposing dug out, shook a few hands and disappeared down the tunnel to contemplate his future and where it all went wrong at the end of his remarkable Arsenal career to the sound of deafening music and singing on a memorable Madrid night he will want to forget.
Savic for Thomas, Correa for Vitolo, Torres for Costa 83.
Chambers for Koscielny 12, Mkhitaryan for Wilshere 68,
Gianluca Rocchi (Italy)