South Africa did not want to execute ICC arrest warrants which would lead to "regime change", a minister said.
Last year, South Africa refused to arrest Sudanese President Omar al-Bashir, who is wanted by the ICC on charges of genocide and war crimes.
He was attending an African Union summit in Johannesburg.
Mr Bashir denies allegations he committed atrocities in Sudan's troubled western Darfur region.
Several media outlets say they have obtained a copy of the "Instrument of Withdrawal", signed by South Africa's foreign minister.