But Diego Simeone’s men, who went into the second leg of the semi-final tie with a three-goal deficit, gave it their best shot at the Vicente Calderon.
They took the lead in just 12 minutes on the night when Saul Niguez got his head on a corner to beat Real keeper Keylor Navas.
Antoine Griezmann then doubled the home side’s advantage moments later from the penalty spot, after Fernando Torres was bundled over in the box.
Some suggested a Barcelona-style comeback could be on the cards as Atletico looked in complete control of the second leg.
However, just before the break, Isco broke the home side’s hearts with a rebounded goal, meaning Atletico had to score three more times to win.
As a result the game began to get more physical and the referee suddenly found he had a lot more to do to stay on top of the tie.
One clash that caught the attention of the TV cameras was the one that took place between Torres and Cristiano Ronaldo.
After the former Liverpool and Chelsea striker followed through on Real keeper Navas, he had a bit of a confrontation with the Portuguese.
It was hard to see what was said between the two stars as Torres moved his head close to Ronaldo, who smiled back at him.
However, Spanish publication Marca believe they have interpreted the exchange after doing a little bit of lip-reading.
And have claimed Torres asked the Real star: « What’s wrong? Clown, » before Ronaldo then replied: « Go home, idiot, » suggesting the tie was over for Atletico.
At this point the referee got between the two players, and that’s when the Portuguese smiled back at his rival.
Torres then apparently concluded the verbal exchange, which took place just before half time, with the response: « Son of a b**** ».