Ramaphosa accepted his resignation and thanked Nene for his time in office.
There has been mixed reaction to Finance Minister, Nhlanhla Nene's confession around private meetings with the Gupta family at the compound in Saxonwold.
Public servants at all spheres and levels of government will have no obligation to responsibly manage state fiscal resources under a compromised minister of finance.
Mcebisi Jonas declined an offer to replace Nhlanhla Nene as South Africa's finance minister, spurring President Cyril Ramaphosa to consider central bank Governor Lesetja Kganyago and one of his predecessors, Tito Mboweni, for the job, according to three people familiar with the matter.
Nene is a key ally of Ramaphosa, who reappointed him finance minister in a cabinet reshuffle shortly after he became president earlier this year. He must also reassure investors and credit-rating companies of credible plans to stabilise debt and revive growth in the mid-term budget on 24 October.
His major achievement at the central bank was building the nation's foreign-exchange reserves to nearly 40 billion dollars from less than 10 billion dollars.
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Ramaphosa's spokesperson Khusela Diko told News24 there was no official comment on the reports yet, while calls to Nene went unanswered.
The alleged breach relates to allegations surrounding a Public Investment Corporation investment in S&S Refinarias‚ reportedly including a $1.7-million "referral fee"‚ which may have benefited the minister's son‚ Siyabonga Nene.
Last week Nene told an inquiry into government corruption he had made numerous visits to the Gupta family, friends of former leader Jacob Zuma accused of unfairly winning state contracts and influencing the firing of ministers.
"It's a measure of his character and commitment to the country that he has made a decision to resign in spite not being implicated in any wrongdoing", the president said.
Zuma ruled for nearly nine years before the governing African National Congress forced him to quit in February and replaced him with his 65-year-old deputy and party leader, Ramaphosa. They fled the country after Mr. Zuma's resignation in February and now live in Dubai. Nene said during his testimony to the inquiry he was sacked in December 2015 for refusing to agree to Zuma's plans to spend billions of dollars on new nuclear plants.