"We lend our support to his family and friends at this painful time", he wrote.
Havelange never received any punishment for this, however, and was allowed to resign from his position as honorary president in 2013.
Havelange who was predecessor to Sepp Blatter at world football's governing body, served from 1974 to 1998.
As head of soccer's highest body for 24 years and with half a century on the International Olympic Committee (IOC), Havelange FIFA a global powerhouse, becoming a central figure in the evolution of today's sporting mega-events.
The greatest leader in the history of the sport in Brazil, Havelange turned 100 years old in May far from the spotlights, preferring isolation instead.
The Brazilian oversaw a 62-fold increase in FIFA's income in nearly a quarter century in charge and made its presidency one of the most powerful positions in sports.
Fifa's financial power greatly increased under Havelange, by 1998 sales for the TV rights for the following three World Cups were worth over £1.3billion.
He had been treated at a hospital in Rio de Janerio in July this year.
A Brazilian businessman with a law degree, Havelange was an Olympic swimmer and water polo player in his youth.
Havelange, whose name is one of those used for the track and field stadium for the Rio Games (Estádio Olímpico João Havelange), played a key role in bringing the Olympics to his country. He welcomed the International Olympic Committee (IOC) in Copenhagen in 2009 by inviting the members to vote to "join me in celebrating my 100th birthday" at the 2016 Olympics in Brazil.
He handed over to Sepp Blatter, whose time at the helm was also dogged with corruption allegations.
He visited 186 countries during his time as Fifa president, and crossed by vehicle the border between the two Germanys in the Cold War era, and saw football transformed into a billion dollar industry.
Havelange was the first non-European head of Federation Internationale de Football Association and its longest serving president, stepping down at age 82.