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.
Adriano had a chance to equalise but his penalty later was saved by Jefferson. Herrera was dismissed for protesting.
"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.
SANTOS IN FINAL
In the Paulista championship, Santos confirmed their status as favourites with a 3-0 win over Sao Paulo at their Vila Belmiro ground and will meet Santo Andre in the final.
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.
The final of the Gaucho championship in the southern state of Rio Grande do Sul will be between bitter rivals Internacional and Gremio.
State competitions precede the Brazilian championship, which starts on May 8.
Follow FFT.com on Twitter
Join FFT.com on Facebook
