Striker Marcelo delighted the Atletico home fans in the 19th minute when he arrowed a shot into the top corner to open the scoring.
The lead lasted 12 minutes until Flamengo midfielder Amaral placed a shot in the bottom corner from outside the area.
Amaral's strike could prove significant with Flamengo taking a crucial away goal to the Maracana Stadium for the second-leg on November 27.
A win or scoreless draw for Flamengo will see them lift the Copa do Brasil for the third time, while Atletico are yet to win the competition.
The winner of the tournament will qualify for South America's premier club competition; the Copa Libetadores.
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