Putin will hold talks with president Thabo Mbeki in the city of Cape Town before addressing parliamentary leaders and signing co-operation deals in healthcare and space exploration.
The Russian leader is travelling with a delegation of Russian business leaders intending to forge closer links between the two countries in the diamond, mining and metal sectors.
The South African foreign ministry has said that the leaders' talks would also include discussions about the Middle East and Iran's nuclear ambitions.
Putin will visit Robben Island where Mbeki's predecessor, Nelson Mandela, spent 18 years as a prisoner of the former apartheid state.
Putin's visit, followed by a trip to Morocco, is seen as part of a drive by Moscow to reassert its diplomatic influence in Africa.
The Soviet Union was a powerful supporter of South Africa's then-underground African National Congress when it was banned by the white racist government.
Mbeki received military training in Russia in 1970, as did other members of the current government.
In an interview published before Putin's arrival, Nkosazana Dlamini-Zuma, South Africa's foreign minister, said co-operation with Russia would enable Africa to "have its voice heard" on international matters.
The volume of bilateral trade between the two countries has grown steadily, with South Africa exporting about $130m worth of goods to Russia in 2004.
Putin's visit also appears to be part of an effort by Mbeki to look beyond Western powers for diplomatic support as well as to broader trade.
Wen Jiabao, the Chinese premier, visited Cape Town several months ago, while Mbeki is due to attend a three-way summit with Luiz Inacio Lula da Silva, the Brazilian president, and Manmohan Singh, the Indian prime minister, in Brasilia later this month.