The Brazilian side defeated Atletico Paranaense 2-0 in the second leg of their cup final, winning 3-1 on aggregate to claim the trophy for the third time
Elias and Hernane scored dramatic, late goals in Rio de Janeiro while both sides had a man sent off as Flamengo left-back Andre Santos and Atletico PR substitute Ciro saw red.
Flamengo's third win puts them equal second alongside Corinthians for most Copa do Brasil crowns, one behind Gremio and Cruzeiro.
Jaime de Almeida Filho's men's first Copa do Brasil win since 2006 also secures their place in next year's Copa Libertadores, though they needed until the 88th minute to go ahead in the tie for the first time thanks to Elias.
Paulinho turned his marker on the side of the area to get to the byeline before cutting back for the former Atletico Madrid attacker to place into the bottom corner.
Santos and Ciro, the latter of whom was introduced in the 73rd minute, both saw red soon after, before Flamengo sealed victory with Luiz Antonio setting up Hernane in the fifth minute of additional time to wrap up the hosts' win.