It is the fourth straight season Atletico have been knocked out of the competition by their local rivals.
Here, AFP sports looks at five key issues facing Atletico if they are to compete once more for their first ever Champions League next season.
Wednesday’s win was inspired by a phenomenal atmosphere for Atletico’s last ever European game at the Vicente Calderon.
After 50 years Atletico will swap their home by Madrid’s Manzanares river just south of the city centre for the new 67,000 capacity out of town stadium to the city’s north.
Doubts remain over whether the Wanda Metropolitano will be ready in time for the start of next season.
However, even when the bricks and mortar are in place, replacing the emotional tide with which the Calderon has carried Atletico to 18 wins in 22 Champions League games over the past four years is a different challenge.
«The same people will be in the Metropolitano,» said Atletico boss Diego Simeone.
«Their emotion and excitement is non-negotiable. It will be their new home.»
Overturn transfer ban
A smiling Simeone looked ahead to an «encouraging» future.
«That final step is still a big one and we need to keep improving,» he added.
However, one factor that threatens to halt Atletico’s progress is a ban preventing them from signing new players until January.
The result of the club’s appeal to reduce the ban to one already served transfer window will be known before the end of the season and will have a huge bearing on Atletico’s ability to make the improvements needed to compete next season.
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