"I have chose to accept his resignation", Ramaphosa told journalists in Cape Town.
Nhlanhla Nene has resigned as finance minister, the presidency announced on Tuesday.
Public servants at all spheres and levels of government will have no obligation to responsibly manage state fiscal resources under a compromised minister of finance.
On Monday, the rand initially sank more than one percent on a newspaper report that Nene had asked President Cyril Ramaphosa to sack him.
Former central bank governor Tito Mboweni was named as Nene's successor - the fifth finance minister in less than three years.
He must also reassure investors and credit-rating companies of credible plans to stabilise the debt and revive growth in the mid-term budget on October 24. He is the kind of person who will be able to take those decisions. His major achievement at the central bank was building the nation's foreign-exchange reserves to nearly US$40-billion from less than $10-billion.
After leaving the Reserve Bank, Mboweni went into business, acting as an adviser in South Africa for Goldman Sachs Group and served as chairman of AngloGold Ashanti and on the boards of other companies.
Newcomer Bilal Asif rocks Australia in first Test
Paceman Peter Siddle gave Australia an early breakthrough when he bowled nightwatchman Abbas for one with a hint of reverse swing. Australia negotiated the 13 overs and were 30/0 at stumps with Usman Khawaja not out on 17 and Aaron Finch batting on 13.
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.
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.
Mr. Nene had committed "errors of judgment" but was not personally implicated in any wrongdoing, Mr. Ramaphosa said in his announcement on Tuesday.
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.
In December 2015, Zuma fired Nene and replaced him with little unknown ANC MP Des van Rooyen.
For the EFF, Nene's position as finance minister is no longer tenable and they are determined to win what they are now calling a battle.