President Ramaphosa has appointed South Africa's fifth finance minister in three years after the latest head of the Treasury resigned over links to the family at the centre of the country's biggest post-apartheid scandal.
Nene admitted to meeting the controversial Gupta family at their Saxonwold residence at the state capture commission of inquiry last week.
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.
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Former central bank chief Tito Mboweni will take over from Nene.
Earlier this week, several economists expressed the view that there would not be major deviations to the mini budget if a new finance minister were to be appointed. "I deeply regret these lapses and beg your forgiveness".
Ramaphosa has vowed to crack down on corruption as he tries to revive the economy and boost declining support for the ruling ANC party ahead of elections next year. He is the kind of person who will be able to take those decisions.
"Look, I bumped into them in public gatherings once or twice, but I never had an engagement and I've never been asked by them to do anything for them", Nene said during the interview (at the 7:47 mark in the below video).More news: Watch Google's Pixel 3 Event Live Stream Right Here
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The rand gained 0.9% to R14.72/$ by 5.25pm in Johannesburg, reversing an earlier decline of as much as 1.4%.
At the graft inquiry, Nene accused Zuma of pushing policies created to benefit the Guptas, including a massive nuclear power expansion programme.
Speaking to Fin24 by phone on Wednesday morning, Rossouw said it was important to honour Nene.
Opposition parties have called for his resignation.
His immediate task will be to reassure markets and ratings agencies that SA is committed to fiscal discipline.
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.
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.