"[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.
The ANC forced Zuma to quit as president in February, clearing the way for his 65-year-old deputy and party leader Ramaphosa to take over.
Last week, Mr Nene told a judge-led inquiry into the alleged influence of the Guptas, known as the Zondo commission, about meetings that he had previously denied.
"I was wrong in meeting the Guptas at their residence", he said. He remained active in politics, and was elected to the ruling African National Congress's decision-making national executive committee at a party congress in December. "I deeply regret these lapses and beg your forgiveness".
"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.
Police probe Interpol president disappearance
Global criminal police organization (Interpol) has asked China for clarification on the fate of their head of MENA Humvee. His wife, who remained in France with their two children, reported her concerns to the police, who launched a probe.
In his speech accepting the resignation, Mr Ramaphosa said that Mr Nene had "defended the cause of proper financial management and clean governance".
The rand and the country's bonds gained as traders welcomed the appointment of Mboweni as finance minister.
Pressure mounts for Nene to step down, but is it good for the economy? 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. The Mail and Guardian reports that his son Siyabonga was involved in a deal with the Public Investment Corporation when Nene was its chairperson.
Jonas told a judicial panel last month that Ajay Gupta offered him the post of finance minister and a R600 million ($40.3 million) bribe in exchange for business concessions. He served as labour minister in the cabinet of former president Nelson Mandela in the mid-1990s and was widely praised for his work as the governor of the South African Reserve Bank from 1999 to 2009.
All eyes will now be on a much anticipated announcement by Moody's on SA's sovereign credit rating on Friday, and Mboweni's maiden medium-term budget policy statement in two weeks.