"These visits do cast a shadow on my conduct as a public office bearer", Nene said in a statement.
But Nene's opponents say he was involved in corrupt deals with the Guptas when he was deputy finance minister and head of the state pension fund.
Mboweni, like mineral resources minister Gwede Mantashe, has been appointed in terms of rules which permit two ministers from outside parliament.
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 announced that Tito Mboweni, a former South African Reserve Bank Governor, will replace Nene as finance minister.
Nene was seen as one of Ramaphosa's closest allies and a leading figure in the government's efforts to tackle graft that allegedly flourished under former president Jacob Zuma, who was ousted in February.
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Both Zuma and the Guptas have denied any wrongdoing. It is a measure of his character that he had taken this decision.
"During his tenure as minister of finance‚ Mr Nene served the people and government of SA with diligence and ability".
Nene was initially hailed as a hero when he told the inquiry that Zuma had fired him in 2015 for "refusing to toe the line" on projects that would have benefited the wealthy Gupta family and others close to the then-president. The announcement led to a strengthening of the South African currency, the rand, which had weakened after earlier reports of Mr. Nene's likely resignation. He served as labour minister in the cabinet of former president Nelson Mandela in the mid-1990s and was widely praised for his work as the governor of the South African Reserve Bank from 1999 to 2009.
Nene is not the only minister in Ramaphosa's cabinet over whom a cloud hangs. The court further ordered her to pay 20% of the legal costs for the Black Sash and Freedom under law - the two non-governmental organisations that took her to court after Sassa said past year that it would be unble to pay social grants from April 2017.
Mboweni clearly loves the social media platform, giving people a glimpse into his life, political thoughts and sense of humour.