Proteas captain Temba Bavuma will travel back to South Africa from India on Thursday.
CSA said this was due to family reasons.
Bavuma will therefore miss South Africa’s two ODI World Cup warm-up matches against Afghanistan on 29 September and New Zealand on 2 October.
Aiden Markram will captain the side in his absence.
The Proteas’ first World Cup match is against Sri Lanka on 7 October.