Nene was seen as one of Ramaphosa's closest allies and a leading figure in the government's efforts to tackle graft that allegedly flourished under former president Jacob Zuma, who was ousted in February.
He previously served as minister of finance from May 25, 2014, until his controversial removal by former President Jacob Zuma on December 9, 2015.
At the graft inquiry, Nene accused Zuma of pushing policies created to benefit the Guptas, including a massive nuclear power expansion programme.
Nene's spokesperson‚ Jabulani Sikhakhane‚ was not available for comment.
"I was wrong in meeting the Guptas at their residence", he said.
"After due consideration of the circumstances around this matter and in the interest of good governance, I have made a decision to accept his resignation", said Ramaphosa.
Netflix Releases ‘Making A Murderer Part 2’ Trailer
The new season will offer up an in-depth look at the post-conviction process and the emotional toll it takes on those involved.
Former SA Reserve Bank governor and newly appointed Minister of Finance Tito Mboweni is highly accomplished and should be able to hit the ground running. "I deeply regret these lapses and beg your forgiveness".
"This is very positive for South Africa because it shows how serious the new government under Cyril Ramaphosa is about dealing with corruption and even the perception of corruption and dishonesty", said Nathan, who was a leading analyst before he founded 10X, a disruptive asset manager. He is urging those ministers and other senior officials to follow Mr. Nene's example by volunteering to give testimony at the national inquiry into corruption so that their conduct can be reviewed.
He told the inquiry he was sacked by Zuma in December 2015 for blocking deals that would have benefited the Guptas, particularly a $100 billion nuclear power deal with Russian Federation that could have crippled Africa's most developed economy.
The finance minister apologised on Friday for his visits to the Gupta family, who are placed at the centre of the state capture allegations. 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.
The alleged breach relates to allegations surrounding a Public Investment Corporation investment in S&S Refinarias‚ reportedly including a $1.7-million "referral fee"‚ which may have benefited the minister's son‚ Siyabonga Nene.
Political parties have rejected Nene's apology. In the testimony, Nene contradicted earlier comments in a television interview in 2016 that he'd encountered the Guptas only at public gatherings.