The casket, draped in a South African flag, was greeted at the airport by a military guard of honour.
A state funeral will be held on Sunday and the coffin is to rest overnight in the grounds of the royal house of Thembu in Qunu.
Mr Mandela, who became South Africa's first democratically elected President, passed away at his Houghton home in Johannesburg last Thursday.
There was a memorial service held for him at the FNB Stadium in Johannesburg on Tuesday and at least 100,000 people saw his body lying in state in Pretoria over the last three days.
The Mandela family expressed heartfelt gratitude for "the excellent arrangements made to enable the people of our country, Africa and the rest of the world to honour our father in a befitting and dignified manner," family spokesperson General Themba Matanzima said.
He said Mandela was at peace, having been bid farewell by the people he so dearly loved.
"This is a constant reminder that Madiba belonged to the people. It was only correct to return him to the people before his getting back to Qunu," said Matanzima.
Ahead of the flight to the Eastern Cape, members of the African National Congress paid their final tributes to the anti-apartheid icon at a ceremony in Pretoria. The event was attended by South African President Jacob Zuma, other ANC leaders and more than 1,000 members of the organisation.
Zuma described Mandela as a "towering figure" and a "democrat who understood the world."
"We will miss him," he said.
Share your memories of Mandela and light a candle for him on his profile at www.remembered.co.za.
Image: © Getty
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