After the first leg ended in a 1-1 draw, midfielder Elias struck in the 86th minute and Hernane hit a second with the last kick of the game to give the Rio club a deserved victory 2-0 in the return.
The win was particularly sweet for manager Jayme de Almeida, who took over at the club in September after a 4-2 league defeat by the same opponents prompted Mano Menezes to resign.
It was a tense match with few moments of skill but that did not bother the vast majority of the almost 70,000 fans who packed the Maracana stadium to see Flamengo lift the trophy for the fifth time.
The result means Flamengo qualify for next year's Copa Libertadores, South America's equivalent of Europe's Champions League.
- Sports & Recreation
- Mano Menezes