President Jacob Zuma and other ANC leaders attended the event, which included a multi-faith service and a musical tribute.
Afterwards, Nelson Mandela’s coffin began the journey by air and road to his ancestral home at Qunu.
It is being accompanied by family members and officials.
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 95-year-old former leader died on December 5.
More than 1,000 members of the ANC, which Nelson Mandela once led, attended the ceremony at the Waterkloof air base in Pretoria.
US civil rights activist Jesse Jackson and Ireland’s Sinn Fein leader Gerry Adams were among the foreign guests invited.
Mourners heard President Jacob 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,” Jacob Zuma said.
The coffin is being flown to Mthatha airport in the Eastern Cape ahead of the burial in Qunu.
The C130 military aircraft carrying the coffin was escorted by two fighter jets after take-off.
Chief mourners from Nelson Mandela’s Thembu clan and family, as well as senior government officials, would be accompanying the coffin, army officials said.
However his widow Graca Machel, and former wife Winnie Madikizela-Mandela, were travelling on a separate flight, in accordance with Thembu tradition.
A military guard of honor will welcome the flight in Mthatha, and the coffin will be placed on a gun carriage and transported to a hearse.
People have been invited to form a human chain to pay their last respects as the cortege makes its way to Qunu.
In Qunu, the Thembu community will conduct a traditional ceremony 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.
On Friday, the South African government said in a statement that “the third day closed with over 50,000 paying their respects to our national icon and first democratically elected president of our country”.
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