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.
Nene, who was widely respected by investors, served as finance minister from 2014 to 2015 until he was sacked by Zuma and was re-appointed by Ramaphosa earlier this year.
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.
While Mboweni has a good reputation, doubts will continue to linger over Ramaphosa's ability to clean up after Zuma's scandal-marred tenure, according to Guillaume Tresca, a senior emerging markets strategist at Credit Agricole CIB from Montrouge, France.
He publicly apologised on Friday.
"These visits do cast a shadow on my conduct as a public office bearer", Nene said in a statement.
Asked repeatedly at a media event in Cape Town whether Nene still enjoyed his confidence and what the future might hold for the finance minister, President Ramaphosa made light of the questions and pretended there was something wrong with his hearing.
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. He is the kind of person who will be able to take those decisions.
Kondlo said Mboweni was likely to take a hard line against public sector wage increases, and could provoke friction with the country's influential trade unions.
The rand gained 0.9% to R14.72/$ by 5.25pm in Johannesburg, reversing an earlier decline of as much as 1.4%.
Both Zuma and the Guptas have denied any wrongdoing.
"I can confirm that he has been in engagement with Mr Nene and I can also confirm that there has been correspondence that has been exchanged between them and they have spoken on the phone... so they have had ongoing conversations".
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".
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".
There are fears however that a new finance minister, three weeks before the tabling of the Medium Term Budget Policy Statement - the so-called mini-budget - could lead to more political turbulence.
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