In his letter asking Ramaphosa to relieve him of his duties, Nene said he was anxious his testimony at the state capture inquiry would detract from his ability to serve and efforts to restore trust in the government.
Meanwhile, Malema - in a written letter to Ramaphosa on Monday - said SA was undergoing serious economic difficulties, and one of the ingredients in an economic recovery was a credible finance minister.
Journalists attending the event were uninterested in the commemorative stamp and immediately questioned the president on the future of Finance Minister Nene - up until now the Ramaphosa has been especially mum on the topic.
The three Gupta brothers, who are allies of former President Jacob Zuma, were implicated by the former anti-graft ombudsman in influencing government appointments and the award of state contracts - allegations they and Zuma deny.
Nene revealed that he had met the Guptas at their Saxonwold home no less than five times during his tenures as deputy finance minister and during the early stages of his first stint as finance minister. "I deeply regret these lapses and beg your forgiveness".
Nene has also been praised by commentators for standing up to Zuma.
"The ANC further commends Comrade Nene for the commitment he has shown to the well-being of the country", ANC national spokesperson Pule Mabe said.
She said there had been ongoing engagements between the two and that Nene had briefed him on the details around his testimony. Many ministers in his cabinet and the previous Zuma cabinets have held meetings with the Guptas, and some have provided favours to the family.
Zuma ruled for nearly nine years before the governing African National Congress forced him to quit in February and replaced him with his 65-year-old deputy and party leader, Ramaphosa.
Until the latest revelations, Mr. Nene was widely seen as a hero of the resistance to corruption.
The communist party praised Nene for refusing to hand South Africa over to what it called the highest bidder, by refusing to sign the nuclear contract, which former president Jacob Zuma wanted to enter into with Russian Federation.
In a separate issue, a South African newspaper reported last week that Mr. Nene's son, Siyabonga Nene, had sought financing from a state agency, the Public Investment Corporation, at a time when his father was the senior government representative on the PIC board. Jonas, Mboweni and Kganyago didn't answer calls to their mobile phones.
The party said his experience will put him in an advantageous position of being able to hit the ground running.