Flamengo rested many of their first-team players ahead of Thursday’s Copa do Brasil tie against Corinthians but were still far superior in front of 61,000 fans.
Vitinho put the home side ahead in the seventh minute when he ran on to a superb through ball to slot home under the advancing keeper Tiepo.
Tiepo saved a penalty from Diego on the stroke of halftime but Lincoln doubled Flamengo's lead five minutes into the second half from close range.
Gum headed a consolation goal for Chapecoense in stoppage time.
The result leaves Flamengo with seven points after four games. Chapecoense have four points from the same number of games.
(Reporting by Andrew Downie; Editing by Toby Davis)
