Ali died at 9:10 p.m. local time in an Arizona medical facility, surrounded by his family. The official cause of death was "septic shock due to unspecified natural causes," said spokesman Bob Gunnell.
Gunnell revealed that Ali was hospitalized last Monday and not Thursday, as was widely reported.
Ali's body is expected to be transported to his hometown of Louisville, Kentucky, where he will be laid to rest on Friday in a public funeral service.
Gunnell said the services will begin with a procession through the streets of the city. The funeral will take place at the KFC YUM! Center and be led by an imam in the Muslim tradition.
Bill Clinton, Billy Crystal, and Bryant Gumbel will be among the eulogizers. A private, family-only burial will follow.
The boxer was admitted to an Arizona hospital for respiratory issues but as the days went by his condition deteriorated. Hana Ali, one of Muhammad's daughters, recounted her father's final moments on Twitter:
"All of use were around him hugging and kissing him and holding his hands, chanting the Islamic prayer. All of his organs failed but his HEART wouldn't stop beating. For 30 minutes ... his heart kept beating. No one had ever seen anything like that. A true testament to the strength of his SPIRIT and WILL!"
Other tributes continue to pour in for the former world and Olympic champion.
President Obama tweeted, "He shook up the world, and the world's better for it. Rest in peace, Champ."
George Foreman, Ali's opponent-turned-lifelong friend, described him as "a fine man" and "royalty."