Brazil striker Fred scored the winner in the 11th minute of "Flu-Fla" derby when he rammed home Thiago Neves's cross on a rain-sodden pitch at the Engenhao.
The victory put Fluminense second in the Brazilian championship standings, one point behind Atletico Mineiro who beat promoted Portuguesa 2-0.
After eight matches, Mineiro have 19 points, Fluminense 18 and Vasco da Gama, who were held 1-1 at Figueirense, 17.
The first Fla-Flu, known as the "Classic of the Multitudes", was played on July 7, 1912. Brazilian football statistics say it holds the world record for the largest crowd at a club match with more than 194,000 watching the Carioca state championship final at the giant Maracana stadium in 1963.
On Sunday, though, with the Maracana closed for 2014 World Cup refurbishment, less than 40,000 went to the match at Rio's Olympic stadium, the Engenhao.
One of the biggest rivalries in Brazilian football began when, six months before the first derby, nine Fluminense first team players left and started a team at Flamengo, which was then only a rowing club. The derby has been played 391 times with Flamengo winning 139 times and Fluminense 124.
The poor weather did not dampen the party atmosphere with a curtain-raiser between teams of former players of both sides before kick-off and a music show at half-time.
Santos beat Gremio 4-2, their first win in the championship, in only their second match with their full first team after concentrating on the Libertadores Cup until their elimination as holders in the quarter-finals by new South American champions Corinthians. Santos have eight points.
On Monday, they will lose striker Neymar, midfielder Paulo Henrique Ganso and goalkeeper Rafael Cabral to the Brazil side taking part in the London Olympics football tournament.
Sao Paulo defeated Coritiba 3-1 with their new coach Nei Franco, who has replaced Emerson Leao, watching from the stands.
On Saturday, Internacional's fans gave new signing Diego Forlan a rousing welcome before their 2-1 home win over Cruzeiro which the Uruguay captain watched from the Beira-Rio stands in Porto Alegre after joining the southern Brazilian club from Inter Milan.
There was an equally spectacular reception by Botafogo at the Engenhao on Saturday for their new recruit, former Dutch international Clarence Seedorf, who landed on the pitch in a helicopter before their kick-off against Bahia, a 3-0 home victory.
