The first ODI will be played in Port Elizabeth on Saturday, 19 January followed by the second match in Durban on 22 January.
Olivier has been rewarded for his performance in the recently-concluded Test series against Pakistan, which the hosts swept 3-0. The 26-year-old picked up 23 wickets from three Tests including three five-wicket hauls and one 10-wicket match haul, but he is yet to make his white-ball debut for the Proteas.
In de Kock's absence, Heinrich Klaasen could be given the wicket-keeping duties and with Steyn rested, Kagiso Rabada is likely to lead the bowling attack.
De Kock and Steyn were included in the original squad, which also featured a maiden ODI call-up for batsman Rassie van der Dussen.
Updated squad for the first two ODIs against Pakistan: Faf du Plessis (c), Hashim Amla, Duanne Olivier, Reeza Hendricks, Imran Tahir, Heinrich Klaasen, David Miller, Dane Paterson, Andile Phehlukwayo, Dwaine Pretorius, Kagiso Rabada, Tabraiz Shamsi, Aiden Markram, Rassie van der Dussen