Fluminense beat Boca 2-1 in extra time to win the annual continental club competition for the first time, thanks to John Kennedy's 99th-minute goal in Rio de Janeiro.
Almiron was appointed by Boca in April, following the departure of Argentine compatriot Hugo Ibarra.
Boca sit seventh in the Primera Division after 27 matches, 17 points behind leaders and long-time rivals River Plate.
"Boca Juniors informs its members and supporters that on Sunday, 5 November, after 9 p.m., Jorge Almiron informed that he and his coaching staff, with a contract in force until the end of the season, had taken the personal decision not to continue as coaches," the club said in a statement.
"Our institution is grateful for the services rendered by all of them and wishes them every success for the future."
