Mourners lit candles during an all night vigil at Robben Island's prison, where Nelson Mandela had spent 18 of his 27 years in jail.
Earlier, there were emotional scenes at the Union Buildings, with reports of some mourners fainting.
The police were on hand to comfort those mourners who were overcome with emotion after seeing the coffin.
The long queues of people hoping to view the body were reminiscent of scenes in 1994 when voters queued in Soweto for the first multiracial elections...
This was the scene in Soweto on polling day in April 1994.
Correspondents who visited the coffin said Mr Mandela's body could be seen through a glass screen, dressed in one of his trademark patterned shirts.
At each end of the casket stood two navy officers clad in white uniforms, with their swords pointing down.
A national day of reconciliation will take place on 16 December when a statue of Mr Mandela will be unveiled at the Union Buildings.
On Tuesday, tens of thousands of South Africans joined scores of world leaders for a national memorial service as part of a series of commemorations for Mr Mandela.
Nelson Mandela's coffin is due to set off for his ancestral home in Qunu, where his state funeral will be held on Sunday ending a week of commemorations.
After leaving the mortuary, the coffin will be taken to an air base for a farewell ceremony for ANC members.
At least 100,000 people have come to see the former South African president's body lying in state in Pretoria over the last three days.
But some had to be turned away because queues were too long.
The 95-year-old former leader died on 5 December.
'Human chain'
The memorial at the Waterkloof air base is expected to start at about 05:00 GMT to allow members of the governing African National Congress to say a last farewell.
The coffin will then be flown to Mthatha airport in the Eastern Cape ahead of the burial in Qunu.
Lt-Gen Xolani Mabangu, from the defence force, said chief mourners among the Madiba clan and Mandela family, as well as senior government officials, would accompany the coffin, the South African Press Association reports.
A military guard of honour will welcome the arrival in Mthatha, and the coffin will be placed on a gun carriage and transported to a hearse.
Local people will form a 'human chain' between Mthatha and Qunu as the procession passes. Once in Qunu, the Thembu community will conduct a traditional ceremony.
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".
Shortly before the lying in state came to an end, at 17:45 local time (15:45 GMT), hundreds of people towards the front of the queue pushed through in the hope to be one of the last through the door.
One police officer told the AFP news agency: "There are too many people. The whole of the Republic of South Africa wants to say goodbye."
Many people waited in the queue for 11 hours for the chance to see Nelson Mandela's body.
Some were angry more time had not been allowed for this ceremonial; others said even if they could not
