Atletico were among 12 clubs who announced plans for the controversial new competition on Sunday.
But the tournament – a rival to the Champions League but with guaranteed participation for its founding members – quickly came under scrutiny.
Anger from fans, players, coaches, governing bodies, governments and the media soon prompted England's 'big six' to back out. Atleti followed, along with Inter and Milan.
Koke, the Atleti captain, posted on his Twitter page on Wednesday: "From the Atletico Madrid squad, we want to convey our satisfaction about the final decision to renounce the Super League project made by our club.
"We will continue fighting to help Atleti grow from our position through the values of effort and sporting merit that have always characterised us, so that all of you continue to see yourself reflected in those signs of identity.
"We continue to work hard, focused on the game tomorrow."
Speaking before Thursday's LaLiga clash with Huesca, Atleti coach Diego Simeone had earlier backed the club both in their decision to pursue the Super League and then to step back.
"I understood that the club was going to decide what was best for the club," he said. "The club has looked at our fans, employees, players, president – the Atletico family."
Simeone added: "We understand that this situation [the withdrawal] is good for everyone. We all belong to football – before being footballers and coaches, we are fans."