The procession entered through the gates of Mandela's homestead accompanied by military vehicles while helicopters flew overhead.
"We are going to miss him so much," said Lusanda Shasha, 17, as the cortege drove out of sight.
Mandela will be buried on Sunday, ending 10 days of national mourning and global tributes for the prisoner-turned-president who transformed his country and inspired the world.
Since Mandela's death at his Johannesburg home on December 5, South Africans have turned out in pouring rain and blistering sunshine to say goodbye to the anti-apartheid icon.
Tens of thousands had packed a soaked stadium in Soweto for a memorial service Tuesday and up to 100,000 people filed past Mandela's open-casket for the three days it was displayed at the Union Buildings in Pretoria.
On Saturday he made his final journey.
After a send-off from his former comrades in the African National Congress, Mandela's remains were flown from Pretoria to his native Eastern Cape.
A C-130 Hercules carrying Mandela's flag-draped casket and escorted by two fighter jets landed in the town of Mthatha, to thousands of waiting mourners and a full military guard of honour.
From Mthatha, Mandela's remains were carried by a funeral cortege to Qunu.
Military personnel lined the route, along with small groups of people singing anti-apartheid songs and songs in praise of the iconic statesman.
