Local media reported earlier this week that Nene had written to Ramaphosa, requesting that he be relieved of his duties in cabinet.
Speaking on Tuesday afternoon at Tuynhuys, Ramaphosa said Mboweni would provide the strong leadership needed at this time. Ramaphosa "must apply the same consistency with other ministers who continue to serve in his cabinet like Malusi Gigaba, Nomvula Mokonyane, and Bathabile Dlamini", it said.
South African President Cyril Ramaphosa accepted the resignation of the country's finance minister Nhlanhla Nene on Tuesday, following what the President described as "errors of judgement".
According to Nene's testimony at the state capture inquiry, it was his firm stance against the nuclear deal which led to Zuma removing him as finance minister in December 2015.
"As former governor of the reserve bank, Mr Mboweni brings to this position vast experience in areas of finance, economic policy as well as in governance", he said.
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.
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"For the country to move forward‚ we need to establish the full extent of state capture‚ identify those responsible for facilitating it and take decisive steps to prevent it happening again", he said.
Ramaphosa said he had received a resignation letter from Nene and had made a decision to accept it. It said Nene's conduct in meetings with members of the Gupta family had been "unethical conduct of lying and misleading the public about his relations with the Gupta criminal syndicate".
The biggest opposition party, the Democratic Alliance, issued a similar call, saying Nene is likely to be the subject of lengthy investigations and that he risks "compromising public confidence" in the National Treasury.
The ANC forced Zuma to quit as president in February after nearly nine years in office, clearing the way for his 65-year-old deputy and party leader Ramaphosa to take over.
At 10.20am, the rand was at R14.6371 to the dollar from R14.5598, at R16.8172 to the euro from R16.7354 and at R19.2597 to the pound from R19.1397.