In a brief written note, the Samaritano Hospital informed that the leader "died at the beginning of the morning" and "sympathizes and offers condolences to family and friends of the sports leader".
He resigned in disgrace as honorary president in 2013.
Havelange served FIFA from 1974 to 1998, the second longest term in the history of world football's governing body. It's reported he had been suffering from respiratory problems in recent months.
FIFA's former president had previously been hospitalized in Rio at least five times since 2012. This was confirmed to the DPA news agency by a spokesperson for the hosptial in Rio de Janeiro, where he was being treated. Federation Internationale de Football Association ethics court judge Hans-Joachim Eckert said that Havelange's conduct was "morally and ethically reproachable".
He was also an International Olympic Committee member from 1963 until 2011, when he resigned due to ill health.
"Thanks to Joao Havelange, football is the world's leading sport - not only from a social, cultural and economic perspective, but also in terms of its political impact".
But he resigned from the International Olympic Committee in 2011 citing health concerns at a time when he faced possible suspension over allegations of payments received from a former marketing firm.
Before moving into sports administration, he was a swimmer, taking part in the 1936 Olympics in Berlin and the 1952 games in Helsinki.
However, the former International Olympic Committee member continued to be honoured elsewhere and Rio's Olympic Stadium bears his name in tribute to the role he played in bringing the Games to Brazil.
He visited 186 countries during his time as Fifa president, and crossed by auto the border between the two Germanys in the Cold War era, and saw football transformed into a billion dollar industry.
Before that Havelange was president of the Brazilian Football Confederation for 15 years during which time his country won the World Cup three times.