Fred Sunday netted in the 11th minute following a Dario Conca assist before substitute Chiquinho fired in after another Conca pass three minutes from time, reported Xinhua.
The result at the Maracana stadium lifted Fluminense to second in Brazil’s Serie A standings with nine points from four matches while Flamengo slipped to 16th with four points.
Fred, who asked to be substituted late in the match, dismissed fears about his fitness just a month before Brazil’s first World Cup match against Croatia.
“The manager (Cristovao Borges) asked the forwards to defend when Flamengo went forward and I wasn’t able to do that so I asked to come off,” Fred said, adding that his exit was due to tiredness, not injury.
“But there’s no such thing as saving yourself for the World Cup,” the former Lyon striker added.
In other matches Sunday, Atletico Mineiro beat Cruzeiro 2-1, Chapecoense lost at home to Gremio 2-1, Corinthians held Sao Paulo 1-1, Bahia drew 1-1 with Vitoria, Coritiba stumbled at home to Sport 1-0 and Santos won 2-0 at Figueirense.