The decision, made by President Cyril Ramaphosa, comes after Nene chose to resign from the post on Tuesday morning following a public outcry sparked by his public apology last week over his multiple meetings with the Gupta family at their private home.
The crisis over the finance minister has thrown a spotlight on Ramaphosa's promise to crack down on corruption and boost economic growth.
President Cyril Ramaphosa announced on Tuesday that he is accepting the departure of Nhlanhla Nene, who submitted a resignation letter earlier in the day after he admitted to having a series of meetings with the Gupta brothers at their mansion in Johannesburg and other locations from 2010 to 2014.
"As a former governor of the Reserve Bank and before that, as Minister of Labour, Mr Mboweni brings with him vast experience in areas of finance, economic policy and governance".
The Guptas, who were friends with former president Jacob Zuma and in business with his son, were implicated by the nation's former anti-graft ombudsman in wielding undue influence over government appointments and the awarding of state contracts - allegations they and Zuma deny.
Former central bank governor Tito Mboweni was named as Nene's successor - the fifth finance minister in less than three years.
Although Nene has since apologised for lying about meeting the Guptas, he chose to step down from his role.
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.
"I have made a decision to accept his resignation", Ramaphosa told journalists in Cape Town.
She said there had been ongoing engagements between the two and that Nene had briefed him on the details around his testimony.
"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.
Both Zuma and the Guptas have denied any wrongdoing.
Nene said during his testimony to the inquiry he was sacked in December 2015 for refusing to agree to Zuma's plans to spend billions of dollars on new nuclear plants.
He previously served as minister of finance from May 25, 2014, until his controversial removal by former President Jacob Zuma on December 9, 2015.
"This principled steadfastness, and his voluntary appearance at the commission of inquiry into state capture as the first sitting Cabinet minister, deserve recognition", SACP spokesperson Alex Mohubetswane said in a statement.
Nene did not answer calls for comment.
Opposition parties have called for his resignation.