Goalkeeper Felipe saved two spot-kicks in the shootout to put Flamengo within one victory of the Rio de Janeiro state title.
As winners of the first stage of the Carioca, if Flamengo beat Vasco da Gama in next weekend's second-stage final there will be no need for a grand final. Vasco beat Olaria 1-0 in Saturday's semi-final.
Disappointed Brazilian champions Fluminense came back down to earth with a bump having qualified for the knockout phase of the Copa Libertadores in midweek with a thrilling 4-2 victory over Argentinos Juniors in Buenos Aires.
Sunday's derby at the Engenhao stadium, played in torrential rain, suffered a delay due to a power failure during the first half.
After play resumed, Fluminense were the better team and deserved their lead when Rafael Moura pounced on a free-kick into the box from Marquinho in the 22nd minute.
Former Fluminense forward Thiago Neves headed Flamengo's 67th-minute equaliser from a long ball into the box by midfielder Willians.
The state championships precede the Brazilian first division championship that starts next month.
Coritiba won title in the southern state of Parana with a match to spare when they beat arch-rivals Atletico Paranaense 3-0 away in the Curitiba derby.
They equalled the Brazilian record of 21 consecutive victories set in 1996 by Vanderlei Luxemburgo's Palmeiras.
In Sao Paulo, the four favourites for the Paulista title reached the semi-finals where holders Santos will meet Sao Paulo and Corinthians face Palmeiras.
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