Ali designed his final memorials himself years before he died, and intended them to be in his home town of Louisville, Kentucky, and open to all.
"He was a gift to his people, his religion, his country, and ultimately, to the world. Ali was an unapologetic fighter for the cause of black people in America," said Sherman Jackson, a leading Muslim scholar who spoke at the service.
"Ali was the people's champion, and champion he did the cause of his people."
More than 14,000 received tickets for the service and millions more were able to watch by live stream. Civil rights activist Jesse Jackson, boxing promoter Don King and Louis Farrakhan, head of the Nation of Islam, were among the high-profile guests in attendance.
Ali joined the Nation of Islam, the black separatist religious movement, in the 1960s, but left after a decade to embrace mainstream Islam, which emphasises an embrace of all races and ethnicities.
The attendees at the service were young and old; black and white; Muslims, Christians and Jews. Some wore traditional Islamic clothing, others blue jeans or business suits. Outside the arena, the term "Jenazah" trended on Twitter as the service started.
"We welcome the Muslims, we welcome the members of other faith communities, we welcome the law enforcement community," Imam Zaid Shakir, a prominent US Muslim scholar, told the crowd. "We welcome our sisters, our elders, our youngsters."
"All were beloved to Muhammad Ali."
The service lasted less than an hour and included prayers and several speakers, including two Muslim women, who described Ali's impact on their own lives, on the world's acceptance of the Islamic faith and as a champion for civil rights.
Mustafa Abdush-Shakur leaned on his cane as he limped into the arena. He came 800 miles from Connecticut despite a recent knee replacement that makes it excruciating to walk.
"This is a physical pain," he said. "But had I not been able to come and pray for my brother, it would have caused me a spiritual pain and that would have been much deeper."
A fellow Muslim who shares the boxing great's name arrived in Kentucky with no hotel reservation, just a belief that his 8,000-mile pilgrimage was important to say goodbye to a person considered a hero of his faith.
Mohammad Ali met the boxer in the early 1970s and they struck up a friendship based on their shared name. The champ visited his home in 1978 and always joked he was his twin brother, he said. He stood weeping at the funeral, a green Bangladeshi flag draped over his shoulder, holding photographs he took of the boxer during his visit, one standing with his family, another of him sprawled on a bed in his home.
The service began with four recitations of "Allahu Akbar" or "God is Great", with silent prayers between a reading from the first chapter of the Koran, a blessing for Abraham, a general prayer for the well-being and forgiveness of the deceased for the next life and a prayer for everyone at the funeral.
The memorials are taking place after a string of assaults on US mosques and Muslims following the Islamic extremist attacks last year in Paris and San Bernardino, California, and anti-Muslim rhetoric in the presidential election.
Organisers of Ali's memorials say the events are not meant to be political. But many Muslim leaders have said they are glad for the chance to highlight positive aspects of the religion through the example of Ali, one of the most famous people on the planet. The global nature of the service - and because it was streamed - offered a window into a religion many outsiders know little about.
"In this climate we live in today, with Islamophobia being on the rise and a lot of hate-mongering going on, I think it's amazing that someone of that calibre can unify the country and really show the world what Islam is about," said 25-year-old Abdul Rafay Basheer, who travelled from Chicago. "I think he was sort of the perfect person to do that."
Muslims typically bury their dead within 24 hours, but the timeline is not a strict obligation, and accommodations are often made, either to follow local customs or, in the case of a public figure like Ali, provide time for dignitaries and others to travel.