The 36-year-old was found dead at the scene of the accident in Aruana, a small province in central Brazil, along with four other people onboard.
The cause of the crash has yet to be determined, but it is reported he was making a routine trip along with a business colleague, a journey he made most weeks.
Fernandao was a favourite during his four years with Internacional, in which he scored 42 goals in 100 games between 2004 and 2008.
The former striker led the club to their first ever Copa Libertadores in 2006 and also captained the side as they won the Fifa Club World Cup that same year.
He started his career with Goias and also enjoyed spells with Marseille, Al Gharafa and Sao Paulo, before returning to Internacional as coach in July 2012, only to be dismissed the following November.