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".
Nene became a divisive figure in the scandal after acknowledging in a hearing that he had visited the Gupta brothers at their homes in Johannesburg, a confession his opponents said tarnished his credentials.
He made a public apology about the matter on Friday.
Nene faced calls to resign after he admitted to visiting the Gupta brothers, friends of the former president Jacob Zuma who have been accused of high-level influence-peddling, and failing to disclose the meetings earlier.
"Through his long tenure as Reserve Bank governor, Mboweni presided over a period of relatively consistent and stable monetary policy and I think the markets would be relatively confident with him at the helm of the South African Treasury". "I deeply regret these lapses and beg your forgiveness".
Nene's departure would deprive Ramaphosa of a close political ally, and a new finance minister - the nation's fifth in less than three years - would have just weeks to deliver a mid-term budget that reassures investors and ratings companies.
The crisis over the finance minister had thrown a spotlight on Ramaphosa's promise to crack down on corruption and boost economic growth.
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"Ramaphosa is cleaning things up and laying a platform so that he is able to campaign confidently when it is election time", Kwandiwe Kondlo, politics professor at the University of Johannesburg, told AFP. 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.
But Nene has also been praised by commentators for standing up to Zuma on crucial issues. Jonas said he had refused, and was warned he would be killed if he spoke of the proposal.
The inquiry, which opened in August, is investigating allegations that Zuma organised the plunder of government departments and public enterprises in a scandal known as "state capture".
"With his experience, the new finance minister will have the advantage of being able to hit the ground running and is, at least, known to market participants, ratings agencies and global financial institutions, who closely follow events in South Africa".
Opposition parties have called for his resignation.
South Africa, Africa's most advanced economy, slipped into recession in the second quarter of this year, and suffers a stubbornly high unemployment of about 28 percent.