The Samaritano Hospital here on Tuesday confirmed that Havelange died of complications resulting from a lung infection, reports Xinhua.
A former Olympic swimmer, Havelange headed FIFA from 1974 to 1998. He also served as an International Olympic Committee (IOC) member from 1963 to 2011.
Under his leadership FIFA grew from a small organisation with a handful of employees to a multibillion-dollar sporting and global brand.
His career was tainted by allegations of corruption, including claims he received kickbacks from FIFA marketing contracts.
Brazil's interim president Michel Temer said in a statement on Tuesday that sport had lost one of its "most expressive leaders".
"Joao Havelange dedicated himself wholeheartedly to the development of sport, principally football," Temer said. "I extend my solidarity to his family and friends at this difficult time."
Ricardo Teixeira, the former president of the Brazilian football confederation, said: "He was the great creator of football as we know it today, from a financial and technical standpoint."
According to Carlos Nuzman, the president of the Brazilian Olympic Committee, Havelange was the most influential official football has known.
"Havelange was one of the biggest figures in world sport and number one in football. When he started at FIFA, football wasn't like it is now. He transformed the game into the most popular sport in the world."
Under his FIFA presidency, the World Cup expanded from 16 to 32 teams.
He was credited for ushering in the era of major sponsorship deals and television broadcasting rights that turned football into a multibillion-dollar global industry.
But Havelange was also stalked by controversy.
In 2010, he and Teixeira were accused of accepting millions of dollars in bribes to award exclusive FIFA marketing rights to Swiss agency International Sport and Leisure (ISL).
He avoided an investigation into the claims, which he denied, by quitting his IOC post in 2011.
Former England striker Gary Lineker caustically said on Twitter on Tuesday: "Joao Havelange, the former FIFA president, has died. Football gave him so much. Yes, you read that correctly."
