The President through the office of Deputy President Thabo Mbeki confirmed to the Sunday Independent newspaper this week that Kerzner, who faces possible bribery charges, did contribute to the ANC's coffers.
"President Mandela has confirmed that Sol Kerzner made the contribution to the ANC while it was fundraising before the elections," Mbeki's spokesman Thami Ntenteni said.
He said the President did not disclose the size of the donation.
The ANC declined to comment late on Saturday night on whether it would apologise to Holomisa.
ANC national spokesman Ronnie Mamoepa said: "The President has spoken the final word on the matter. We will not make any further comment on it. The issue is sub judice."
Holomisa also claimed that Kerzner had funded Deputy President Thabo Mbeki's 50th birthday party and suggested that Mbeki and Sport Minister Steve Tshwete had accepted favours from the hotel magnate for protection against possible bribery charges.
Mbeki and Tshwete instructed lawyers last week to warn Holomisa to desist against making such allegations or face possible legal action.
In a statement issued from its Johannesburg head office two weeks' ago the ANC said the allegations were "not only blatantly false but also malicious and defamatory".
Holomisa faces an internal disciplinary inquiry this Wednesday arising from statements he made to the Truth commission in Port Elizabeth implicating fellow ANC national executive member and Public Enterprises Minister Stella Sigcau in corruption when she was a former Trankei government minister.
He alleged that Sigcau was among Transkei officials who accepted a R50,000 cut from a R2 million payment Kerzner made to former Transkei prime minister George Matanzima for exclusive gambling rights.
The three disciplinary charges against Holomisa relate to misconduct, bringing the ANC into disrepute and conduct unbecoming of an ANC member or elected representative.
He was also stripped of his deputy ministerial portfolio by President Mandela, although no reasons were given for the dismissal.
Holomisa may face additional disciplinary charges for subsequent statements made.
When the ANC denied his claims that Kerzner had funded it, Holomisa then disclosed that President Mandela was the source of his information.
Holomisa told Sapa President Mandela had approached him at the Carlton Hotel in early 1994 and told him that Kerzner was willing to contribute R2 million.
Kerzner had also asked whether the ANC could assist in the criminal proceedings pending against him in the Transkei, the nominally independent homeland that Holomisa ruled at the time and which was reincorporated into South Africa after the 1994 general elections.
President Mandela had asked whether anything could be done about the matter and had also approached him after the elections about Kerzner's case, Holomisa said.
The President confirmed this week that the Carlton Hotel meeting with Holomisa had taken place.
"There was a meeting in 1994 between the President and Holomisa," Ntenteni told the Sunday Independent.
"It was a routine meeting and Sol Kerzner was not on the agenda. But the controversy surrounding Kerzner and the charges against him were prominent in the media so President Mandela did ask Holomisa about the Kerzner affair.
"He was interested because Kerzner had made a donation to the ANC. Holomisa briefed the President on the matter, but subsequent to that meeting there has been no follow-up with the Transkei attorney-general or any other person to influence the outcome of the case," Ntenteni said.
Transkei attorney-general Christo Nel earlier told Sapa that no ANC leader had approached him to drop charges against Kerzner.
Holomisa was not immediately available for comment.