It is coach Muricy Ramalho's fourth title in five years after winning three in a row with Sao Paulo from 2006 to 2008.
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A goal just past the hour from striker Emerson ensured the 45,000 home fans who packed the Enganhao stadium could celebrate the end of a 26-year wait for the title by their team which escaped relegation only on the final day of last season.
The title completes the climb of Fluminense from the third division in 1999, having suffered successive relegations.
"It's very difficult to try to explain all this. These fans deserved this title. It's 26 years, not 26 months or 26 weeks, now it's time for the Fluminense fans to celebrate after a long time without this joy," Emerson told reporters.
Fluminense, regarded as the most elite of the four big clubs in Rio de Janeiro and who had waited the longest for the title, finished with 71 points from 38 matches.
Cruzeiro overtook Corinthians to finish second two points behind after a 2-1 home win over Palmeiras. Corinthians were third with 68 points after being held 1-1 away to relegated Goias.
Sunday's last match was much harder than expected against a committed young Guarani side who prevented Fluminense from creating attacking moves and Emerson's goal calmed the nerves of the faithful.
DISAPPOINTING CORINTHIANS
The man at the heart of Fluminense's campaign was diminutive Argentine playmaker Dario Conca, who played in all their matches in the championship and is favourite to win the Player of the Year award on Monday.
He often led the team during long injury absences of captain Fred and former Barcelona and Chelsea midfielder Deco, the club' main recruit this season. Deco missed Sunday's match through injury.
Corinthians were the big disappointment of the championship and, having exchanged the lead several times with Fluminense, finished without a title in their centenary year.
The top three go into next year's Libertadores Cup with holders Internacional and Copa Brasil winners Santos.
Fourth-placed Gremio will also qualify for South America's elite club competition if Goias fail to win the final of the Copa Sudamericana, the region's Europa League equivalent, against Independiente of Argentina.
Goias go into this week's second leg in Buenos Aires with a 2-0 lead.
