The cremation follows a moving memorial service attended by some 1, 500 people in northern Johannesburg, including prominent people in politics, culture and business.
Makeba's ex-husband, South African jazz musician Hugh Masekela, offered a final trumpet solo for the singer who came to be known as Mama Africa.
South Africa marked its loss with flags flown at half mask over public buildings.
During a musical career that began in the 1950s, Makeba stood out as arguably the most popular singer from the African continent. She was barred from returning home by the apartheid government in 1960 for her anti-apartheid activities and returned only after apartheid began crumbling in the early 1990s.
Makeba spent a subsequent three decades in exile, living in various countries, highlighting the plight of victims of racism and social injustice. She also became a United Nations goodwill ambassador.