The classified documents surrounding the agreement between the countries and cited by the Guardian were uncovered by Sasha Polakow-Suransky, an American academic, during research for a book, the newspaper said.
The defence ministers also signed a broad-ranging agreement governing military ties between the two countries that included a clause declaring that "the very existence of this agreement" was to remain secret.
Sunday's report said that the documents were proof that Pretoria wanted the weapons to keep neighbouring states and other enemies from attacking them.
The report also said Israeli authorities attempted to keep the South African government from declassifying the documents.
A statement issued on Monday by the office of Peres, now Israel's president, rejected the newspaper's report.
"There exists no basis in reality for the claims published this morning by The Guardian that in 1975 Israel negotiated with South Africa the exchange of nuclear weapons," it said.
|Yossi Melman, Israeli journalist, discusses the claims made by author Polakow-Suransky
"Unfortunately, The Guardian elected to write its piece based on the selective interpretation of South African documents and not on concrete facts.
"Israel has never negotiated the exchange of nuclear weapons with South Africa. There exists no Israeli document or Israeli signature on a document that such negotiations took place."
However, Ian Black, Middle East editor of the Guardian, says the significance of the revelation is that it provides documentary proof that Israel was prepared to sell nuclear warheads to South Africa.
"This shows that Israel was prepared to be a proliferator of nuclear weapons and encourage the spread of them around the world," he told Al Jazeera.
"We have had definitive evidence since the 1980s that Israel certainly has nuclear weapons, but it's one thing to have weapons, this shows that Israel was going to sell weapons to another country.
"Something that was previously known perhaps as a rumour or suspicion, has now been confirmed as fact - that the Israeli government had strong relations with the apartheid government and that Israel was planning to sell nuclear weapons."
According to the Guardian, the minutes of the meeting on March 31, 1975, record that: "Minister Botha expressed interest in a limited number of units of Chalet subject to the correct payload being available."
The document then records: "Minister Peres said the correct payload was available in three sizes. Minister Botha expressed his appreciation and said that he would ask for advice."
Polakow-Suransky is also quoted as saying that Israel's offer to equip South Africa with atomic weapons was the result of the regime's need for a military deterrent and for potential strikes against neighbouring states.
"South Africa's leaders yearned for a nuclear deterrent - which they believed would force the west to intervene on their behalf if Pretoria were ever seriously threatened - and the Israeli proposition put that goal within reach," the Guardian quoted Polakow-Suransky as writing in his book published in the US this week, The Unspoken Alliance: Israel's secret alliance with apartheid South Africa.
But the alleged deal did not go through, according to Polakow-Suransky, although Israel did reportedly provide South Africa with 30 grams of tritium, the substance which provides thermonuclear weapons with a boost to their explosive power.
The delivery, according to the Guardian, was enough to build several atomic bombs.
Waldo Stumpf, a former chief executive officer of South Africa's Atomic Energy Commission, told Al Jazeera that Botha "was quite adamant that the South African nuclear weapons programme was there for political reasons and was never there for technical reasons".
Allister Sparks, a political commentator and former editor of South Africa's Rand Daily Mail newspaper, told Al Jazeera that the confirmation of a relationship between Israel and the apartheid regime came as no surprise.
"Israel will obviously come out and deny this evidence and label anyone who takes it seriously as being anti-Semites," he said, "but this makes it more difficult for Israel to hold the respect of the world."
|Documents show South Africa wanted missiles as a 'deterrent' [The Guardian]
The documents confirm accounts by Dieter Gerhardt, a former South African naval commander, jailed in 1983 for spying for the Soviet Union.
After his release following the collapse of apartheid, Gerhardt said there was an agreement between Israel and South Africa called "Chalet", which involved an offer by Israel to arm eight Jericho missiles with "special warheads".
According to the paper, Gerhardt said these were atomic bombs. But until now there has been no documentary evidence of the offer.
The existence of Israel's nuclear weapons programme was revealed by Israeli whistleblower Mordechai Vanunuto the Sunday Times in 1986.
He provided photographs taken inside the Dimona nuclear site but provided no written documentation.
According to the Guardian, Israel "pressured" the present South African government not to declassify documents obtained by Polakow-Suransky.
"The Israeli defence ministry tried to block my access to the agreement on the grounds it was sensitive material, especially the signature and the date," he told the Guardian.
"The South Africans didn't seem to care; they blacked out a few lines and handed it over to me. The ANC government is not so worried about protecting the dirty laundry of the apartheid regime's old allies."
Israel is widely believed to be the only nuclear-armed power in the Middle East, with around 200 warheads, but it has a policy of neither confirming nor denying that.
It has refused to sign the nuclear Non-Proliferation Treaty or to allow international surveillance of Dimona in the southern Negev desert.
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