The match was halted after just three minutes when fans of Independiente Medellín lit flares and threw objects onto the pitch.
The disruption, which occurred at the Atanasio Girardot stadium in Medellín, was reportedly an organised protest against the local club's management due to poor results.
CONMEBOL, the governing body of South American football, officially cancelled the Group A match more than an hour after its initial suspension.
Under CONMEBOL Disciplinary Code, Flamengo is expected to be awarded a 3-0 victory, as Independiente Medellín's fans were deemed responsible for the match's abandonment.