The former Brazil boss only took charge of the Brasileiro Serie A side in July, after the sacking of Abel Braga, who led Fluminense to the title last year.
However, Sunday's defeat against Corinthians has left the Rio-based outfit 18th in the standings with just five rounds remaining.
"At the behest of club president Peter Siemsen, coach Vanderlei Luxemburgo will not continue in his role as coach of Fluminense," read a club statement released on Monday.
"Fluminense appreciates the efforts of the coach and his coaching staff."
Fluminense, who have not won a league game since September, next face Nautico at the Maracana on Thursday.