After trailing 3-1 at half-time and having defender Alvaro sent off in the 63rd minute, Flamengo enjoyed an inspired performance at the Maracana from their two strikers Adriano and Vagner Love.
"We play for each other, we're both top level players and we're chasing the same objective, to get to the World Cup," Adriano said as both strikers talked to reporters.
Fluminense scored twice in the opening half hour through Andre and Argentine midfielder Dario Conca and could have had more goals as they were in complete control but were without injured striker Fred.
Adriano pulled one back with a penalty after Juan was brought down but defender Cassio restored Fluminense's two-goal advantage following a goalmouth melee from a corner.
Flamengo were a changed team in the second half and had equalised by the 54th minute with goals by Vagner Love and midfielder Kleberson.
Adriano, top scorer in the 2009 Brazilian championship, won the match for Flamengo when they were a man short. He tapped in from a cross by Vinicius Pacheco eight minutes from time and completed his hat-trick with a stoppage-time breakaway.
Corinthians, a man short from the ninth minute when Roberto Carlos was sent off, withstood strong pressure from Palmeiras to beat them 1-0 in their Paulista (Sao Paulo) championship derby.
Already without Ronaldo, who is nursing a thigh muscle injury, Corinthians lost their other World Cup winner when the former Real Madrid left back was shown a straight red for a bad tackle from behind on Joao Arthur.
"For me, it was harsh, but what can I do?" Roberto Carlos told reporters as he left the field. "What a referee mustn't do is spoil a 'classico' like that."
Corinthians went ahead two minutes before the sending off with a headed goal from Jorge Henrique and had goalkeeper Felipe to thank for a string of saves as they beat biggest rivals Palmeiras for the first time in three years.
Two minutes from time, Palmeiras midfielder Cleiton Xavier was sent off for dissent, his second bookable offence.
Paulista title holders Corinthians snatched the lead in the standing from Santos, who beat Oeste 2-0 on Saturday after a pre-match visit from Robinho who has returned to his first club on a six-month loan from Manchester City.
Internacional beat Gremio 1-0 in Porto Alegre in their big derby in the Gaucho (Rio Grande do Sul) championship.
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