But signals that the post-apartheid government and Tel Aviv are cosying up to each other have brought outrage from the country's hardline pro-Palestinian lobby driven largely by Moslem groups.
In the week before Deputy Prime Minister Ehud Olmert's arrival, the umbrella Palestinian Support Group (PSG), the Congress of South African Trade Unions (COSATU) and the South African National non-governmental organisation Coalition embarked on a protest campaign.
Protestors, many among them prominent campaigners in apartheid-era liberation movements - insisted allowing him into the country would amount to a "betrayal of the Palestinian people."
They urged Pretoria to isolate Israel through economic, cultural and sport boycotts not unlike the treatment meted out to South Africa's under apartheid.
In Pretoria, deputy Foreign Minister Aziz Pahad stressed in a meeting with pro-Palestinian groups on the eve of Olmert's arrival, was trying to be impartial by engaging both Tel Aviv and Palestinian groups.
Olmert, who is also trade and industry minister and was accompanied by a business delegation, signed a protection of investment agreement in Johannesburg on Wednesday.
The PSG has rejected suggestions that South Africa's decision to improve trade relations with Israel may in itself be a "trade off" with a view to bring about an end to the plight of the Palestinians.
Speaking after the signing ceremony marked by protests, Olmert said he was delighted at Pretoria's decision to host him despite the controversy his visit had sparked.
Israel's trade with South Africa in fields such as mining, agriculture and water would open doors for the tiny state to the rest of the continent, he suggested.
Using trade with the African continent for leverage over Israel might be Pretoria's strategy for encouraging dialogue between Israeli's and Palestinians, according to Professor Hussein Solomon, director of the Pretoria-based Centre for International Political studies.
South African groups aligned to the Palestinian cause, Hussein noted, were among their more radical supporters, people with "war mentality" who saw the complexed conflict in "black and white".
In 2001 Pretoria initiated a series of discussions with Palestinian and Israeli groups that centred around sharing its transition from white minority rule to democracy through a negotiated settlement.
It has offered the experience and views of its own role players, past and present, in talks with officials from the Palestinian Authority and recently Israel's Likud Party.
Olmert, whose visit had been agreed to three years earlier, first toured the country at the height of apartheid in 1978 as a young Knesset member.