The Brazilian Serie A team were travelling to Medellin for the final of the Copa Sudamericana when their plane lost power and came down at around 10.15pm local time.
The death toll currently stands at 76, with players, staff members and journalists among those that lost their lives in an incident that has shocked the world of football.
Boeck, who previously played for Sporting Lisbon, turned 32 on Monday, and his agent said that he stayed in Brazil.
Antonio Araujo is quoted by The Sun as saying: "The club gave him permission to avoid travelling. It has been a great relief at a time of deep sadness and tragedy which has hit everyone in football very hard.
"Marcelo went with his family to the Chapecoense stadium where found the other players who had not travelled. I talked to him and he is deeply saddened by everything that has happened."
It is understood that Atletico Nacional, who were due to face Chapecoense in the final of the Copa Sudamericana, have asked for their opponents to be handed the trophy.