Large numbers of people lined the roads in the rural region to pay their respects as the cortege passed by.
A state funeral will be held on Sunday, December 15, for South Africa’s first black president, who died on December 5.
The coffin was flown from Waterkloof airbase in Pretoria on a C130 military aircraft, escorted by two fighter jets.
In line with tribal custom, Nelson Mandela’s grandson Mandla accompanied him on the journey, speaking to his coffin to tell him he was on his way home to rest.
It arrived in Mthatha, 450 miles away at 13:37 local.
To solemn music, the coffin draped in a South African flag was moved by a military guard of honor and placed in a hearse to begin the 20 miles journey to Qunu, where Nelson Mandela had said he wanted to be buried.
People waving flags and cheering and singing – in places 10 to 12 deep – lined the route taken by the cortege through Mthatha town to pay their last respects.
Tears as well as smiles could be seen on the faces of onlookers.
The cortege then drove through the gates of the Mandela homestead in Qunu, where it will rest overnight in the grounds of the royal house of Thembu.
The Thembu community will conduct a traditional ceremony – including songs and poems about Nelson Mandela’s life and his achievements – in a giant white marquee that has been specially erected.
Some 4,000 people, including presidents from Africa, several prime ministers, the Iranian vice-president, and the Prince of Wales, are expected to attend.
However, Archbishop Desmond Tutu – a long-time friend of Nelson Mandela – has cancelled arrangements to fly to the Eastern Cape for the funeral after saying he had not been invited.
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