This is after he took to the stand in the judicial commission of inquiry into state capture, and admitted to having met the Gupta family on several occasions - this is contrary to what he told news channel eNCA back in 2015.
Nene is a key ally of Ramaphosa, who reappointed him finance minister in a cabinet reshuffle shortly after he became president earlier this year.
Former reserve bank governor Tito Mboweni has been appointed finance minister after President Cyril Ramaphosa accepted Nhlanhla Nene's letter of resignation. Five months after refusing to sign a letter of guarantee that would have given the project to Russia's state-controlled nuclear energy company, Mr. Nene was sacked from Mr. Zuma's cabinet and was briefly replaced by a pro-Gupta minister.
Analysts had also started welcoming the news, saying that the move was good news because it showed Ramaphosa's leadership was serious about making a clean break with the past.
"These visits do cast a shadow on my conduct as a public office bearer".
The Guptas are a trio of Indian-born brothers accused of fraudulently profiting from vast government contracts and energy and transport deals under Zuma, who ruled from 2009 to 2018.
The rand gained 0.9% to R14.72/$ by 5.25pm in Johannesburg, reversing an earlier decline of as much as 1.4%.
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The visitors trailed by 555 runs at the close, with Roston Chase (27 not out) and Keemo Paul (13 not out) in the middle and showing some fight.
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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.
But Nene has also been praised by commentators for standing up to Zuma on crucial issues.
Commenting on the state capture inquiry, Ramaphosa said it was critical that the commission had the means and opportunity to effectively fulfil its mandate.
The country's main opposition party, however, said it was anxious about some of Mboweni's social media posts during his period away from politics and described them as "a little looney" and "at odds with government policy".
The party said his experience will put him in an advantageous position of being able to hit the ground running.
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.
"The Medium-Term Budget Policy Statement‚ which is supposed to be a statement to build confidence among all important economic role players‚ cannot‚ and should not‚ be delivered by a minister who was part of the Gupta criminal syndicate".