A state funeral will be held on Sunday for Mr Mandela, who died on 5 December.
At least 100,000 people saw the former South African president’s body lying in state in Pretoria over the last three days, but some had to be turned away.
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, 700 km (450 miles) away at 13:37 local (11:37 GMT).
To solemn music, the coffin draped in a South African flag was moved by a military guard of honour and placed in a hearse to begin the 32km journey to Qunu, where Mr 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.
However, some people expressed their frustration that the convoy did not stop, so they had no chance to view the coffin as people in Pretoria had.
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 BBC’s Milton Nkosi in Qunu said it was a powerful moment for the local community to see their liberator coming home.
The Thembu community will conduct a traditional ceremony – including songs and poems about Mr 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.
Archbishop Tutu, said he had no wish to “gatecrash what was billed as a private family funeral”. But the South African government – which Archbishop Tutu has criticised – later said the churchman had been invited.
“This is not an event where you need credentials and I hope a solution can be found,” said government spokesman Mac Maharaj. “He’s an important person and I hope ways can be found for him to be there.”
Ahead of the flight to the Eastern Cape, members of the African National Congress paid final tributes to Nelson Mandela at a ceremony in Pretoria.
President Jacob Zuma, other ANC leaders and more than 1,000 members of the organisation which Mr Mandela once led, attended the event at the Waterkloof air base.
It included a multi-faith service and a musical tribute.
Mourners heard President Zuma pay his own tribute to Nelson Mandela, calling him a “towering figure”, “a man of action” and a “democrat who understood the world.”
“Yes, we will miss him… He was our father, he was our guardian. He was something special.”
“We’ll always keep you in our hearts,” Mr Zuma said.