Simoes, who led Jamaica to the 1998 World Cup, was dismissed a matter of hours after his team won 3-0 at Nacional de Patos in the Copa Brasil.
He was expected to be replaced by Brazil's 1994 and 2006 World Cup coach Carlos Alberto Parreira, who quit South Africa for family reasons two years before he was due to lead them at the 2010 finals.
"Rene did a beautiful job with Fluminense in 2008," director Alexandre Faria told the club's website.
"Unfortunately the team has not got into gear this season and we reached the consensus that it's necessary to change the leadership."
Simoes took over in October when Fluminense were in the relegation zone of the Brazilian championship with only 10 matches to play. They eventually finished 14th in the 20-team table.
His dismissal came after a poor series of results in the Rio de Janeiro championship, one of the regional tournaments which form the prelude to the 2009 season.
Simoes also coached Trinidad & Tobago in the 2002 World Cup qualifiers and returned for a second stint with Jamaica last year. In between he led the Brazilian women's team to the silver medal at the 2004 Olympic Games.
