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.
Fluminense took an early lead with a header by defender Leandro Euzebio before Flamengo finished the first half 2-1 up with goals from striker Deivid and defender David.
In end-to-end action with plenty of chances for both sides, Flu striker Rodriguinho (pictured) scored two equalisers, in the 64th and 72nd minutes either side of a third Flamengo goal from midfielder Renato.
"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.
Third-placed Cruzeiro, who have 41 points, lost the chance to overtake Flu when they were held 2-2 by Botafogo at the Enganhao on Saturday after going 2-1 up with goals by their diminutive Argentine playmaker Walter Montillo.
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.
SCOLARI DISMISSED
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."
Santos were held 0-0 at home by Guarani with teenage forward Neymar watching from the stands after coach Dorival Junior had the 18-year-old him dropped indefinitely from the squad over recent indiscipline.
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