The 36-year-old was travelling with four other people, all of whom were killed when the helicopter came down en route to Goiania after taking off from his home in the city of Aruana.
Goiania-born Fernandao began his career with local club Goias before signing for Marseille in 2001.
After a loan stint at French rivals Toulouse, he returned to Brazil in 2004 to play for Internacional - where he won the Rio Grande do Sul title twice, the Copa Libertadores and the FIFA Club World Cup.
He went on to play for Al Gharafa in Qatar, Goias and Sao Paulo, before retiring in 2011, when he became a director at Internacional and later the club's coach.
An Internacional statement read: "We are immensely saddened by the untimely death of our idol.
"What stays with us are the glorious memories of a striker who honoured the Internacional jersey with his spirit of leadership and was one of the most important players in the club's 105-year history."