Corinthians, who had pulled level with Flu in midweek when they beat them 2-1, went top on Saturday with a 3-0 win over bottom team Gremio Prudente for their 13th victory in 22 matches.
After 23 rounds, Corinthians have 44 points, two more than Fluminense whose form has slumped in recent weeks with only six points from seven matches, and a game in hand.
"This leaves a bitter taste because we had victory in our hands," Flamengo coach Silas, whose side are 15th six points above the relegation zone, told reporters.
The match was watched by a small crowd of 19,000 at the Enganhao stadium. "Fla-Flu" clashes attract more than three times that number of fans to the Maracana, now closed for 2014 World Cup refurbishments.
Big Uruguayan striker Sebastian Abreu, noted for his cheekily chipped penalty shootout decider in Uruguay's World Cup quarter-final against Ghana, equalised from the spot.
Former Brazil and Portugal coach Luiz Felipe Scolari was sent to the stands for the second time in two months for protesting at refereeing decisions during his Palmeiras team's 2-0 defeat by Sao Paulo in their city "clasico".
"It's time for someone to lift the microphone and say I'm being persecuted," said Scolari, whose side are 13th with 29 points.
"It's soon not going to be worth remaining on the side of the pitch. Better to stay away from the bench where I won't have any dismissals. If that's what they want, that's what I'll do."
