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.
The winner of the tournament will qualify for South America's premier club competition; the Copa Libetadores.
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