The three-match ODI series is due to get underway on January 19.
The decision has been taken keeping in mind the high workload on Rabada and to make sure he recovers in time for the scheduled New Zealand tour next month.
"Proteas seam bowler, Kagiso Rabada, has been released from the team for the Betway One-Day International (ODI) series against India due to high workloads over a sustained period of time and the need for him to recover prior the outbound Test series against New Zealand next month," Cricket South Africa (CSA) said in a release.
The hosts didn’t name Rabada’s replacement but asked George Linde, who was a part of the Test squad, to stay in the bio-bubble with the team as an extra spin-bowling option.
"No replacement will be brought in for him as there is an extended squad in place in the Bio-Secure Environment (BSE), but George Linde has been retained from the Test team as an extra spin-bowling option for the series," CSA added.
Rabada was the leading wicket-taker in the three-match Test series against India, which the Proteas won by 2-1. The right-arm pacer claimed 20 scalps at an average of 19.05.
The three-match ODI series is due to get underway on Wednesday (January 19) at the Boland Park in Paarl.
Updated South Africa ODI Squad:
Temba Bavuma (captain), Keshav Maharaj (vice-captain), Quinton de Kock (wicketkeeper), Zubayr Hamza, Marco Jansen, Janneman Malan, Sisanda Magala, Aiden Markram, David Miller, Lungi Ngidi, Wayne Parnell, Andile Phehlukwayo, Dwaine Pretorius, George Linde, Tabraiz Shamsi, Rassie van der Dussen, Kyle Verreynne.