Four survivors - three players and a radio commentator - were introduced at Rio's Olympic stadium before the game.
Striker Dudu scored the only goal when he headed home after the break.
Chapecoense drew 2-2 against Palmeiras on Saturday in their first game since the tragedy.
Only six of the 77 people on board the LaMia flight carrying the Chapecoense team to Colombia for their Copa Sudamericana final survived the crash on 28 November. Of those on board, 43 were players and staff.
The club has rebuilt its squad, with most of its 22 new players arriving on loan from other clubs.
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Brazil beat Colombia 1-0 in a friendly that raised more than £300,000 for the families of the Chapecoense players and staff who were killed in a plane crash in November.