Paulinho and Hector Cantero scored first-half goals during Sunday’s match before Bruno Rangel pulled one back for the hosts late in the second half, Xinhua reported.
Kayke then put the result beyond doubt by finding the target two minutes from time at Arena Conda.
Flamengo remain fourth in the standings with 41 points while Chapecoense have slipped to 14th.
In Porto Alegre, Alexandre Pato was on the scoresheet in Sao Paulo’s 2-1 victory over Gremio. Rogerio also netted for the visitors before Everton struck in second-half injury time for Gremio.
Also on Sunday, Corinthians beat Joinville 3-0, Ponte Preta defeated Santos 3-1, Cruzeiro and Atletico Mineiro drew 0-0, Vasco da Gama overcame Atletico Paranaense 2-0, Avai accounted for Goias 2-1 and Sport beat Fluminense 1-0.