In a nationally televised address, Ramaphosa said he accepted Nene's resignation because of "errors of judgment" as a result of a controversy surrounding Nene's testimony in an ongoing graft inquiry in South Africa.
The crisis over the finance minister had thrown a spotlight on Ramaphosa's promise to crack down on corruption and boost economic growth.
Nene is facing calls to resign after he admitted to visiting the Gupta brothers, friends of scandal-plagued former president Jacob Zuma who have been accused of high-level influence-peddling, and failed to disclose the meetings earlier.
At the graft inquiry, Nene accused Zuma of pushing policies created to benefit the Guptas, including a massive nuclear power expansion programme.
"After due consideration of the circumstances around this matter and in the interest of good governance, I have made a decision to accept his resignation", said Ramaphosa. "I deeply regret these lapses and beg your forgiveness".
The party said it would have been better if Nene had acknowledged all the Gupta meetings from the onset but said the important thing was that he had taken responsibility for his weakness and resigned.
"These ministers have demonstrated the same disregard of ethical conduct shown by Nene and like Nene they too have undermined parliament's accountability mechanisms", the EFF said in a statement.
She said there had been ongoing engagements between the two and that Nene had briefed him on the details around his testimony.
Until the latest revelations, Mr. Nene was widely seen as a hero of the resistance to corruption.
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. 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.
The IFP said it was concerned that Ramaphosa did not use the opportunity to also get rid of controversial ministers Bathabile Dlamini and Malusi Gigaba, but welcomed Mboweni's appointment.
Opposition leaders, however, noted that Mr. Mboweni had been active on social media in the past and had once posted a tweet in which he called for state ownership of 40 per cent of all mining companies. 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.