They picked up a valuable away goal from their 1-1 draw at the Emirates and triumphed with a 1-0 win at the Estadio Metropolitano on Thursday.
Former Chelsea striker Diego Costa scored a first-half winner for the Rojiblancos.
Costa keeps haunting Arsenal
Costa left Chelsea and re-joined Atleti in January and hadn’t initially had the best of returns to Spain, scoring only six goals in 19 appearances in all competitions.
However, the 29-year-old has always been Arsenal’s nemesis and this was no different in Thursday’s semi-final.
Right from the beginning of the game, Costa imposed himself on Arsenal’s defence and used his physical qualities to fight off the challenge of Hector Bellerin to break the deadlock.
In seven past meetings with Arsenal, the Brazilian-born Spanish international has won five and scored four times.
Arsenal need to strengthen the defence
The Gunners once again were weak in defence and could have quite easily conceded more than one goal against Madrid, barring some heroics at the back from Calum Chambers.
The England international did well after replacing the injured Laurent Koscielny – who is ruled out for the season and 2018 World Cup in Russia – but the likes of Shkodran Mustafi, Nacho Monreal, and Hector Bellerin were a disappointment.
Bellerin was guilty of failing to track Costa prior to the Spanish striker scoring the opener. The Arsenal defender was also physically outclassed.
Whomever replaces Arsene Wenger as Arsenal manager should focus on rebuilding the defence.
Arsenal average in attack
Unlike at the Emirates, Arsenal looked far from an attacking threat against Atleti at the Metropolitano.
The Gunners barely created any clear-cut opportunities and couldn’t get a shot away when they did work an opening.
Moreover, Bellerin and Monreal appeared to be neutralised, with very few of their crosses reaching the feet of an Arsenal teammate in the box.
The north Londoners had just one attempt on goal – Granit Xhaka’s hopeful long-range strike.