"We will miss him, He was our leader in a special time," President Jacob Zuma said at a ceremony attended by about 1,000 people at an air force base in Pretoria, CNN reported.
Mandela's coffin was loaded onto a military plane which flew it to Mthatha in Eastern Cape Province, the closest town to the village of Qunu where Mandela grew up.
He will be buried there Sunday in a state funeral. Some 4,000 people are expected to be in attendance, including African presidents, former U.S. President Bill Clinton and former Secretary of State Hillary Clinton, and Britain's Prince Charles, the BBC reported.
About 400 family and friends will walk to Mandela's grave site, CNN reported.
Overnight Saturday, the coffin will lie in state on the grounds of the royal house of Thembu, from which Mandela was descended. A traditional ceremony will be performed by members of the Thembu clan.
Maki Mandela, the Nobel Peace Prize winner's oldest daughter, said her father wanted to buried in Qunu because of his fond memories of growing up there, CNN reported.
"He really believed this is where he belonged," she said.
"Even when my father was in jail, he had the most fondest memories of Qunu. And he really wanted to die here," Mandela added.
Some 100,000 people are estimated to viewed Mandela's body as it lay in state for three days in Pretoria, the BBC said. On the last day, Friday, the South African government said more than 50,000 people stood in line for up to 11 hours to pay their respects.