"Flu" opened an unassailable 10-point lead over Gremio, who climbed to second with a 2-1 home win over Sao Paulo in Porto Alegre while Ronaldinho's Atletico Mineiro were held 1-1 at Vasco da Gama in Rio and dropped to third 11 points off the pace.
Captain Fred led his team to their second title in three years amassing a record points haul of 76 in 35 matches with the potential to add up to nine more.
"It's a mixture of happiness with emotion. The squad is marvellous, these fans follow us always," Fred told reporters after being lifted on the shoulders of team-mates.
"I thank God, the [club] board, the players, the [coaching] staff, the fans... only a player's family knows the effort we all put in."
Palmeiras held the match at Presidente Prudente in Sao Paulo state far from their city base for fear of trouble from angry fans, who had already staged violent demonstrations as their team totters on the brink of relegation.
Fred opened the scoring on the stroke of half time, stroking the ball home from the rebound after goalkeeper Bruno parried a shot from winger Wellington Nem.
Fluminense went two up in the 54th minute with an own goal by Palmeiras defender Mauricio Ramos as he tried clear a Fred cross.
FRED WINNER
Palmeiras hit back with two goals in four minutes just past the hour, the first from Argentina striker Hernan Barcos with the equaliser coming from a header by Patrick Vieira, the namesake of the former Arsenal and France midfielder.
Fred, overlooked by Brazil coach Mano Meneses this year, volleyed the winner from Jean's right cross two minutes from the final whistle to take his championship tally to 19.
"A very good team with a poor atmosphere don't become champions. A good team with an excellent atmosphere is what we managed to build here and that's how we got to the title," coach Abel Braga told reporters.
"This is a team with no individual [stars]. Even Fred, who is captain and top scorer, is just another player in this squad."
It was Fluminense's fourth national title, third in the Brazilian championship first played in 1971, since they also won a tournament in 1970 that has since been recognised by the sport's governing body CBF as being national in its scope.
Thousands of fans converged on the clubs headquarters in the southern Rio district of Laranjeiras to celebrate, causing a major traffic jam in an area normally quiet on a Sunday night.
Two teams have already been relegated, Atletico Goianiense and Figueirense. Four teams will go down.
