"We wish Minister Mboweni well as he journeys through the mammoth task of steering our economy in the right direction".
Ramaphosa declined to answer reporters' questions about Nene at the release of a new postal stamp at his Cape Town office on Tuesday.
Ramaphosa said Mboweni, the former Governor of the Reserve Bank, brings in much-needed leadership.
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".
"It is a measure of his character and his commitment to the national interest that he has taken this decision to resign in the wake of errors of judgment‚ even though he has not been implicated in acts of wrongdoing".
"I am confident that Mr Mboweni will provide that leadership‚" he said. He made a public apology about the matter on Friday.
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The Gupta family have been accused of using their friendship with Zuma to siphon off billions of rand in state funds and of inappropriately influencing cabinet appointments.
The crisis over the finance minister had thrown a spotlight on Ramaphosa's promise to crack down on corruption and boost economic growth.
Mboweni, who went into exile during apartheid, trained as an economist and served for four years as labor minister in former President Nelson Mandela's cabinet after apartheid ended in 1994. 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. He became the first black governor of the SA Reserve Bank in August 1999 and served for just more than 10 years until November 2009.
"[He] is, at least, known to market participants, ratings agencies and global financial institutions, who closely follow events in South Africa", the DA's Shadow Minister of Finance David Maynier said in a statement.
South Africa's Finance Minister Nhlanhla Nene looks on ahead of the Judicial Commission of Inquiry probing state capture in Johannesburg, South Africa October 3, 2018.
The visits occurred when he was deputy finance minister and also finance minister before Zuma fired him from that post in December 2015, Nene testified.