De Kock suffered a left wrist injury whilst batting during the second ODI at Centurion on Sunday and needs two to four weeks to make a full recovery.
South Africa were already without the services of star player AB de Villiers and Faf du Plessis, who both suffered finger injuries.
Cricket South Africa has named no replacement for de Kock in the ODI squad.
De Kock had a forgettable Test series with the bat and had scored 34 and 20 in the first two ODIs.
India won the first ODI at Durban by six wickets and the second ODI by nine wickets to take a 2-0 lead in the six-match series.
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