Former Olympic swimmer Havelange, who was at the centre of the bribery and corruption scandal during his spell at the helm, died in hospital in this year's host city, Rio. "The institution sympathises with family and friends of the sports director".
Along with former FIFA Ex-Co members Ricardo Teixeira and Nicolas Leoz, Havelange was found to have taken millions of dollars in illegal payments throughout the 1990s from the former marketing partner of world football's governing body.
He resigned in disgrace as honorary president in 2013.
Under Havelange the World Cup expanded from a 16-nation event focused on Europe and a few South American sides to the planet-wide sporting festival it has become. He was hospitalized for more than two months, including several weeks in intensive care, in 2012 because of an infection in his right ankle.
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.
Over those 24 years, Havelange was credited for vastly growing the appeal of world football, boosting its development across every continent. This July, he was admitted to the Samaritan Hospital in Rio de Janeiro due to pneumonia.
Havelange was able to parlay what he learned in Brazilian sport to build a coalition among football associations in Africa, Asia, and the Americas.
As the IOC's longest-serving member, Havelange stood down in 2011 with an ethics hearing pending over the ISL affair. All three were subsequently swept up in corruption investigations by Swiss and USA authorities last year that also brought the end of Blatter's 17-year presidency.
The Rio 2016 Olympic stadium, where athletics and football matches are being played at the Games, was named after Havelange.
He was re-elected president six times, capitalizing on his contact-building across world football.
The United States was awarded the 1994 World Cup during Havelange's rule, in 1988.
Havelange became the first non-European to take on the Federation Internationale de Football Association presidency and earned support from the developing world.