Namibia, Botswana and Zimbabwe have also sold off their stocks
South Africa has held the world's biggest legal sale of ivory for almost 20 years.
The auction in Pretoria of more than 51 tonnes of elephant tusks was sanctioned by the UN body which oversees trade in endangered species.
The tusks sold for $142 per kilo, netting the government $6.7m (£4.2m) -less than expected.
The South African government has been condemned by conservation groups and other African countries for the sale.
Namibia, Botswana and Zimbabwe have all sold off their own ivory stocks over the past two weeks.
The ivory can only be sold to officially approved buyers from China and Japan and the money has to be spent on conservation.
They are not allowed to export the ivory, and the Convention on International Trade in Endangered Species (Cites) says it will monitor trade to make sure companies are not mixing illegally sourced ivory with the legal shipments.
The BBC's Jonah Fisher went to a large warehouse at a secret location in Kruger National Park in South Africa where the hundreds of elephant tusks were stored.
Some of them were small and stacked on shelves, while others lay on the floor - great curved pieces of ivory - over two metres (6.5ft) long.
APPROVED SALES IN 2008
Botswana: 43.68 tonnes
Namibia: 9.2 tonnes
South Africa: 51,12 tonnes
Zimbabwe: 3.75 tonnes
All of the elephants that the tusks came from either died naturally or were culled as part of a population control programme.
In previous sales, the ivory had been sold for $150 (£94). South Africa expected to make about $8m (£5m) from the auction.
Wanda Mkutshulwa, from South African National Parks, told the BBC that she welcomed the sale.
"We're seeing less and less funds being channelled towards conservation and yet... there is so much work that still needs to be done."
Critics of the auction - such as Kenya - say creating a legal ivory market encourages elephant poaching and makes it easier for illegal tusks to be sold.
However, data collected by the wildlife trade monitoring network Traffic shows that seizures of illegal ivory fell in the years following the last legal sale in 1999, says the BBC's environment correspondent Richard Black.
The ivory trade was banned globally in 1989 because poaching was decimating elephant populations. These sales and the 1999 sale are the only exceptions.
Last month, the internet site eBay banned virtually all products containing ivory after lobbying from animal welfare groups.