The Brazil international delayed a decision on his club future until after the Copa America and both parties have now agreed not to extend his contract, which expired at the end of June.
Atleti have overhauled their squad since the end of last season and though he had been open to the prospect of another campaign under Diego Simeone, Filipe Luis agreed the time has come for a change.
🔴⚪🔴 | #GraciasFilipe— Atlético de Madrid (@atletienglish) July 21, 2019
🛡 3⃣3⃣3⃣ games in Red & White! Atleti legend and former left-back Clemente Villaverde presented @filipeluis with a well-deserved plaque ❤⚪❤☺ #AúpaAtleti pic.twitter.com/e0Tlmgdyev
"We had a conversation and decided this is best for the club and for me," Filipe Luis said at his farewell announcement on Sunday.
"The relationship is great, the doors are open. We waited for the right moment to announce it. We both have a clear conscience.
"I made myself available for whatever was needed. We decided that it was best to go our separate paths."
The left-back praised his successor and compatriot, Renan Lodi, as the best Brazil had to offer in his position.
After more than a decade in Europe, which included a season at Chelsea in between his two stints with Atleti, Filipe Luis now appears set to return to his homeland.
"I have not signed any contract," he said. "I will make the decision in the next few days.
"I have been a Flamenguista since I was young. Leaving Atletico is not an easy decision to make, but I want to end my career in Brazil
"Some things are missing. We are conversing. You always have to listen to Flamengo."