"South Africa remains a signatory to the ICC in line with a resolution of the 55th National Conference of the ANC – held in December 2022 – to rescind an earlier decision to withdraw from the ICC," the presidency said in a statement.
"The December resolution was reaffirmed at a meeting of the National Executive Committee of the ANC during the weekend of 21 to 24 April 2023."
Ramaphosa said on Tuesday that the ruling African National Congress would aim to repeal South Africa's membership of the Hague-based court, which hears cases of genocide, war crimes and crimes against humanity.
But on Wednesday, Ramaphosa's office said he had made a mistake.
The presidency said on Wednesday that South Africa would work towards establishing an African continental criminal court that would complement the ICC as a court of last resort.
The ANC decided at its national conference in December that South Africa should abandon a legislative process to pull out of the ICC and try to effect changes to the organization from within.
Putin is due to visit South Africa in August for a summit of the BRICS group of emerging economies comprising Brazil, Russia, India, China and South Africa. As an ICC member, South Africa would be required to detain him.
Putin has not travelled abroad since the ICC warrant was issued. He has made only one trip outside the former Soviet Union - to Iran - since launching the invasion of Ukraine last year.