Nobel Peace Prize winner Tutu died a week ago, aged 90, after a life spent fighting injustice.
His ashes were “interred at St. George’s Cathedral in a private family service early today”, an Anglican Church statement said.
Archbishop Thabo Makgoba placed his remains under an inscribed memorial stone before the high altar.
He urged South Africans to “use this opportunity to turn a new page.
“Let us commit ourselves… to the radical, the revolutionary change that he advocated,” Makgoba said.
“Let us live as simply as he lived, exemplified by his pine coffin with rope handles.”
Some 20 members of Tutu’s family, led by his widow “Mama Leah” were present.
Famed for his modesty, Tutu had left instructions for a simple, no-frills funeral with a cheap coffin, followed by an eco-friendly flameless cremation.
Family, friends, clergy and politicians had attended a requiem mass on Saturday with President Cyril Ramaphosa leading the tributes.
“Our departed father was a crusader in the struggle for freedom, for justice, for equality and for peace, not just in South Africa… but around the world as well,” said Ramaphosa.
“While our beloved (Nelson Mandela) was the father of our democracy, Archbishop Tutu was the spiritual father of our new nation”, lauding him as “our moral compass and national conscience”.
Under apartheid, the white-minority government cemented its grip imposing laws based on the notion of race and racial segregation, and the police ruthlessly hunted down opponents, killing or jailing them.
With Mandela and other leaders in prison for decades, Tutu in the 1970s became the emblem of the anti-apartheid struggle.
He campaigned relentlessly abroad, administering public lashings to the Western world for failing to slap sanctions on the apartheid regime.
After apartheid was dismantled and South Africa ushered in the first free elections in 1994, Tutu chaired the Truth and Reconciliation Commission, which exposed the horrors of the past in grim detail.
He would later admonish the ruling African National Congress for corruption and leadership incompetence.
Tutu’s moral firmness and passion went hand-in-hand with self-deprecatory humour and a famously cackling lau