In 1984 Tutu won the Nobel Peace Prize for his non-violent opposition to apartheid. A decade later, he witnessed the ends of that regime and he chaired a Truth and Reconciliation Commission, set up to unearth atrocities committed during those dark days.
The outspoken Tutu was considered the nation's conscience by both Black and white, an enduring testament to his faith and spirit of reconciliation in a divided nation.
Tutu was diagnosed with prostate cancer in the late 1990s and in recent years he was hospitalized on several occasions to treat infections associated with his cancer treatment.
"The passing of Archbishop Emeritus Desmond Tutu is another chapter of bereavement in our nation’s farewell to a generation of outstanding South Africans who have bequeathed us a liberated South Africa," President Cyril Ramaphosa said.
"Desmond Tutu was a patriot without equal."
The presidency gave no details on the cause of death.
Tutu preached against the tyranny of white minority and even after its end, he never wavered in his fight for a fairer South Africa, calling the Black political elite to account with as much feistiness as he had the white Afrikaners.
In his final years, he regretted that his dream of a "Rainbow Nation" had yet to come true.
"Ultimately, at the age of 90, he died peacefully at the Oasis Frail Care Centre in Cape Town this morning," Dr Ramphela Mamphele, acting chairperson of the Archbishop Desmond Tutu IP Trust and Co-ordinator of the Office of the Archbishop, said in a statement on behalf of the Tutu family.