Attended by relatives of the deceased, the ceremony took place in a hangar at the Waterkloof Air Force Base in Pretoria. The hangar was draped in black and a large number of chairs were set out in front of a stage with flowers.
The formal proceedings included a prayer and scripture reading, the National Anthem and a moment of silence.
The names of the deceased were read out one by one by Director General in the Presidency, Cassius Lubisi.
Uniformed South African military personnel solemnly played the "Death March" as the four forensic pathology trucks carrying the bodies departed the airport and made their way to provincial mortuaries.
Uncontrollable cries could be heard from the bereaved family members while others collapsed. Counsellors from various government departments were seen consoling the family members.
The televised 45-minute ceremony was watched across the country.
Earlier on Sunday, a cargo aircraft carrying 74 of the 85 who will be repatriated landed at the Air Force Base, under strict security control.
The aircraft was received by Chairperson of the Inter-Ministerial Task Team set up to oversee the repatriation process, Jeff Radebe, along with Health Minister Aaron Motsoaledi and Social Development Minister Bathabile Dlamini.
A total of 116 people, 81 of them South African, died on 12 September when a guesthouse belonging to the Synagogue Church Of All Nations in Lagos collapsed.
South Africa has agreed to repatriate the remains of three Zimbabweans and one DRC national who were using South African travel papers, thus bringing the total number of people to be repatriated to 85.
Twenty-six people who were injured in the collapse returned to South Africa a month ago, only one remains in hospital while the others have been reunited with their families.
Director General Lubisi, in reading the names of the deceased, said 12 victims were from the Eastern Cape, 2 from the Free State, 22 were from Gauteng, 23 from Mpumalanga, 13 from Limpopo, 6 from the North West, 5 from KwaZulu-Natal and 2 from the Western Cape.
The only one province not affected by tragedy was the Northern Cape.
Deputy President Cyril Ramaphosa, who addressed the formal ceremony on behalf of government and the people of South Africa, said the people who died were not mere statistics but people who lived among us.
"They were people who had hopes and dreams for their children... they were our brothers and sisters, our compatriots and fellow South Africans."
The Deputy President said the families should take solace in the fact that all South Africans share in their bereavement and that the dead can rest in peace in the land of their birth.
"As a nation, and as a people, we share in your grief and your sorrow. Your pain is incalculable, we know."
He added that the people of South Africa and Nigeria were united in sorrow.
Remaining bodies to be returned to SA
Governments from both countries will make sure the bodies that are still in Nigeria are brought back without further delay.
The Deputy President then thanked all those involved including Minister Radebe, Nigerian President Goodluck Jonathan, officials in the Inter-Ministerial Committee and medical experts involved in the repatriation process.
Minister Radebe, who travelled to Nigeria this week to meet with authorities there with a view to expedite the process, said the repatriation process had been traumatic, especially for the families of the 11 victims whose remains were still in Nigeria.
He thanked his team and the Nigerian authorities for their efforts.
Minister Radebe read a tribute to the Department of Health's Pieter Fourie, who died after he contracted malaria. He was part of the team of experts who went to Nigeria to assist with the process of preparing the bodies for repatriation.
At the end of the formal reception ceremony, the bodies were transported to the closest government Forensic Pathology Services mortuaries in the different provinces.
From there they will be transported to the government mortuary closest to the place of burial where they will be received by their next-of-kin.
Individual families will proceed with their own private funeral arrangements.
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