Botafogo, who had also won the first phase of the championship, took the lead with a penalty by Argentine forward German Herrera in the first half before Flamengo equalised a minute before halftime through Vagner Love.
Botafogo had lost the final to Flamengo in the last three seasons but their victory on Sunday meant there was no need for a title decider. It was the first time since 1998 the same team has won both phases.
Flamengo, the national champions, had Brazil striker Adriano back after missing four games with a rib injury but they came up against strict marking tactics by Botafogo's former South Africa Joel Santana.
Flamengo had Chile's Claudio Maldonado sent off for giving away the decisive penalty which Abreu lobbed in off the underside of the bar.
"I'd never missed a penalty and it had to happen now," Adriano told reporters.
"When two big teams face each other, the fight always ends with a knockout. The victory wasn't built today," said Santana, who has masterminded Botafogo's recovery after taking charge following the team's 6-0 defeat by Vasco da Gama in January.
Teenage forward Neymar boosted his campaign for a place in Brazil's World Cup squad with two goals, the first with the apparent help of his hand and the other a penalty after he was fouled. Playmaker Paulo Henrique scored the third for Santos.
In the Mineiro championship in the state of Minas Gerais, Cruzeiro were surprisingly eliminated by Ipatinga, who will meet Vanderlei Luxemburgo's Atletico Mineiro, Cruzeiro's arch-rivals from the city of Belo Horizonte, in the final.
