South Africans have two words to welcome new Finance Minister Tito Mboweni, "Sha Sha".
Nene has become a divisive figure after testimony he gave at an inquiry into allegations of corruption by the Guptas, in which he admitted to the previously undisclosed visits.
He publicly apologised on Friday.
"It's a measure of his character and commitment to the country that he has chose to resign in spite not being implicated in any wrongdoing", the president said. Nene did not answer calls for comment.
Alluding to Nene's refusal to give the green light to the Russian nuclear deal, which was being pushed through by former president Jacob Zuma and which would have indebted South Africa to the European state for years to come, Ramaphosa praised Nene saying: "He served our people under very hard circumstances and often coming under pressure but he consistently defended the cause of proper financial management and clean governance".
Mboweni is a member of the ANC's national executive committee, one of the ruling party's highest decision-making bodies.
The rand gained 0.9 percent to 14.71 per dollar by 5:25 pm in Johannesburg, reversing an earlier decline of as much as 1.4 percent on the news.
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Treasury spokesman Jabulani Sikhakhane referred Reuters to the presidency for comment.
Economics professor at the University of Johannesburg, Fiona Tregenna, says the president made the right choice in accepting Nene's resignation.
In a written letter to Ramaphosa, Malema argued that the country, whose economy is in recession, had very serious challenges that needed a credible finance minister to address them.
Nene has also been praised by commentators for standing up to Zuma.
Nene told the inquiry that it was his belief that his refusal to sign off on a massive nuclear deal ultimately led to his dismissal in 2015 - which saw the rand crash.
Pressure has been piling on finance minister Nhlanhla Nene to resign, following his disclosure to the state-capture inquiry commission, that he had met the Gupta brothers between 2010 and 2013.
The main opposition Democratic Alliance party welcomed Mboweni's appointment, saying he was a safe pair of hands.