Rafael Marques scored the only goal five minutes before halftime after a long-range shot by Lucas was deflected into his path.
Botafogo were awarded a penalty in the 80th minute for a foul on Nicolas Lodeiro but former AC Milan and Real Madrid midfielder Seedorf spoiled an otherwise inspirational performance by firing against the crossbar.
Sunday's match was the final of the tournament's second stage but, as Botafogo had also taken the first stage, they won the championship automatically.
The tournament is one of the numerous regional championships, each with different and often bafflingly complex formats, which kick off the marathon Brazilian season.
Corinthians reached the Paulista (Sao Paulo state) championship final by beating Sao Paulo 4-3 on penalties after a goalless semi-final.
The shootout ended in controversy as Corinthians striker Alexandre Pato saw his team's final kick saved by Rogerio Ceni only for the referee to order a re-take, which he converted amid angry protests from Sao Paulo.
Paulo Henrique Ganso and Luis Fabiano both missed for Sao Paulo whose players surrounded the referee to protest at the end.
Corinthians will face Santos in the two-leg final after they also won on penalties against Mogi Mirim following a 1-1 draw.
Former Brazil coach Dunga's Internacional won the Gaucho (Rio Grande do Sul) championship, beating Juventude 4-3 in yet another penalty shootout after a goalless draw.
The win meant that Inter took the second stage of the competition and the title as they had already won the first stage.