This is after he took to the stand in the judicial commission of inquiry into state capture, and admitted to having met the Gupta family on several occasions - this is contrary to what he told news channel eNCA back in 2015.
Ramaphosa has thanked Nene for his time in the ministry.
New Finance Minister Tito Mboweni clearly loves Twitter - and he's remarkably good at it for a "pensioner". He became the first black governor of the SA Reserve Bank in August 1999 and served for just more than 10 years until November 2009.
The rand and the country's bonds gained as traders welcomed the appointment of Mboweni as finance minister.
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Up and down they ( Liverpool ) are the best team in the world in these transitions, offensive, defensive, it is built for that. They are incredibly quick and we controlled them outstandingly, but we didn't create too much.
The Guptas, who built a vast business empire in the mining and media industries in South Africa after forging a partnership with the son of former president Jacob Zuma, are now under criminal investigation on corruption allegations. Nene did not answer calls for comment.
Nene's Gupta meetings have damaged the reputation of a man once thought to be "clean" compared to those ANC politicians who have been implemented in state capture.
"The initial selling reaction on the rand on reports that its finance minister has asked to be sacked will encourage investor caution that South Africa could be in store for another round of political risk", said Jameel Ahmad, head of currency strategy at FXTM.
But he had accepted the resignation because Mr Nene feared his testimony "detracted from the important task of serving the people of South Africa as we work to re-establish public trust in government", Mr Ramaphosa said. Jonas, Mboweni and Kganyago didn't answer calls to their mobile phones.
Mboweni, the nation's fifth finance chief in less than three years, will have to oversee an economy that's fallen into recession and help Ramaphosa rebuild confidence battered by nearly nine years of mismanagement under former President Jacob Zuma. Ramaphosa has said combating graft is one of his top priorities, and he's replaced a number of other officials implicated in wrongdoing.