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.
Smooth stadium transition
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.
Keep Simeone satisfied
Simeone himself has been the key figure in Atletico's emergence from a sleeping giant to European power over the past five-and-a-half years.
One of his former clubs Inter Milan, who sacked Stefano Pioli on Tuesday, look set to launch a new offensive for the Argentine, who reduced the length of his contract from 2020 to 2018 earlier this season.
Keeping Simeone this summer is an absolute must amidst the other upheaval surrounding Atletico.
Maintain young core
Retaining Simeone will also make it far easier to hold onto a host of rising young stars.
Atletico are likely to be powerless over top-scorer Antoine Griezmann's ability to leave with a number of clubs willing to meet his 100 million euro ($109 million) buyout clause.
However, the Frenchman has consistently recognised his loyalty to Simeone for turning him into one of the world's best players and only he will be able to convince Griezmann into staying for another season.
Generally Atletico's age profile is promising with Jan Oblak (24), Jose Maria Gimenez (22), Lucas Hernandez (21), Saul Niguez (22), Koke (25) and Yannick Carrasco (23) all with the prime years of their career to come.
The riches of the new stadium and a fifth straight year of Champions League football for the first time in their history also mean Atletico are now in a position where they don't need to sell.
"Clone" ageing leaders
However, two of Atletico's most vital players, Diego Godin and Gabi, are 31 and 34 respectively.
"We have to clone some players," said Simeone. "The hearts of some of the players we have are huge and they transmit so much passion to their teammates."
Atletico are well-stocked in Godin's position at centre-back thanks to Gimenez, Hernandez and Stefan Savic and the Uruguayan still has a few more years at the top left in him.
A long-term replacement for Gabi, who came through the Atletico academy, is a tricker task not only for his ability, but his leadership and love of the club.