The governments agreed to boost economic, technical and commercial ties.
Trade between South Africa, the continent's economic powerhouse and a major gold-producing country, and China reached $240 million in the first 11 months of 2006, an increase of 34.5 per cent from the previous year.
Protocols on the sanitary conditions for the export of grapes and tobacco from South Africa to China were also signed, as well as for the import of pears and apples to South Africa from China.
However, there has been growing criticism over rising Chinese domination in South Africa and the rest of the continent.
South African trade unions have complained that Chinese textile imports are devastating the domestic industry, forcing the two governments to sign a memorandum of understanding aimed at restricting imports.
But at a joint news conference between Hu and Thabo Mbeki, his South African counterpart, there were no sign of tensions.
Mbeki said China was one of his country's most important trading partners.
"President Hu's visit emphasises the determination on both sides to develop the relations we have had for some time. China is one of our most critical, most important economic partners globally," he said.
He also thanked China for the assistance it has given South Africa as a newly elected non-permanent member of the UN Security Council and the role China has played on the continent.
Hu committed himself to establishing a free trade area.
"In recent years economic co-operation between China and South Africa and southern Africa has grown very rapidly to the benefit of both sides. We are all very positive about the establishment of a free trade area," he said.
Hu is expected to deliver an address at the University of Pretoria on Wednesday and hold talks with Chinese business and community leaders.
He then heads to Mozambique and the Seychelles.