The former Chelsea and Atletico Madrid wing-back was dismissed last night despite Fla's victory on Monday night against Madureira.
Fla won 8-0 on Monday night to beat Madureira 11-0 on aggregate to book their place in the Campeonato Carioca final.
However, Luis has been removed after poor performances in other domestic Cup competitions.
An official club statement confirmed: "Clube de Regatas do Flamengo informs that, as of this Tuesday (3), Filipe Luís will no longer be in charge of the professional team. Ivan Palanco (assistant coach) and Diogo Linhares (physical trainer) are also leaving the club along with him.
"Flamengo thanks former player and coach Filipe Luís for everything that was achieved and shared during this journey. The club wishes him success and the best of luck in the continuation of his professional career."
Luis' next job is expected to be in Europe after guiding Flamengo to victory in the Copa Libertadores last year.