The 36-year-old was one of five people aboard a helicopter that went down on Friday night in Aruana province, central Brazil. There were no survivors.
A spokesperson for the fire service said Fernandao was making a routine business trip. He had been due to appear on Sport TV during the World Cup.
The striker captained Internacional to their first Copa Libertadores title in 2006, then the FIFA Club World Cup, and scored 42 goals in 100 games the club.
He won a solitary cap for his country in 2005.
Fernandao spent three seasons in France early in his career, featuring for Marseille and Toulouse.
He became Internacional coach in July 2012, but was sacked after just four months.
Brazilian President Dilma Rousseff was among those to pay tribute, tweeting: “Fernandao will be missed.”
She added: "A club world champion.on the pitch, Fernandao was an example of character off the pitch."
Alexandre Pato, a team-mate of Fernandao at Internacional, also tweeted his condolences.
Meanwhile former Arsenal and Brazil midfielder described Fernandao as “an idol of Internacional and of football”.
The country hosts the 2014 World Cup, which starts next Thursday in Sao Paulo.
- Sports & Recreation
- Dilma Rousseff
- FIFA Club World Cup