President Ramaphosa has appointed South Africa's fifth finance minister in three years after the latest head of the Treasury resigned over links to the family at the centre of the country's biggest post-apartheid scandal.
Weekend reports indicated that Nene's future as finance minister was on shaky ground following his admission to the meetings, with some claiming Gauteng finance MEC Barbara Creecy could be his replacement.
Briefing the media, Ramaphosa said he had accepted Nhlanhla Nene's resignation.
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The 59-year-old minister is expected to steady a ship on the rocks after Nene's state capture inquiry bombshells, where he admitted to a relationship and to meeting the controversial Gupta family at their Saxonwold home.
Earlier this week, several economists expressed the view that there would not be major deviations to the mini budget if a new finance minister were to be appointed.
It had received a battering under Mr Zuma's presidency. "I deeply regret these lapses and beg your forgiveness".
His resignation was a measure of his commitment, in the wake of errors of judgment, said Ramaphosa, "even though he has not been implicated in any act of wrongdoing himself".
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Nene, who publicly apologized for not previously reporting the visits to the Gupta brothers, has not made any statements confirming or denying the report by Business Day newspaper. Five months after refusing to sign a letter of guarantee that would have given the project to Russia's state-controlled nuclear energy company, Mr. Nene was sacked from Mr. Zuma's cabinet and was briefly replaced by a pro-Gupta minister.
It said the issue was likely to be raised at a meeting of the ruling African National Congress party later on Monday. The Guptas have been accused of having improper influence over former president Jacob Zuma and his executive, as well as control of operations at state owned enterprises, which they used to loot billions of rand from South African taxpayers.
"Mr Mboweni takes on this responsibility at a critical time for our economy, as we intensify co-operation among all social partners to increase investment, accelerate growth and create jobs on a substantial scale".
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