The Proteas, who had already won the series, made 301/8 after they won the toss and chose to bat, but the game was abandoned before India could start their run chase.
New top-order star Quinton de Kock, the Man of the Series, played another mature innings.
The 20-year-old opener became the fifth player to smash three consecutive ODI tons and set a record for the most runs in a three-match series with a total of 342.
The hosts were reduced to 28/3 in the eighth over, but skipper AB de Villiers joined De Kock in the middle and the duo set about stabilising the innings against a determined Indian attack.
De Kock, the Man of the Series, fell for 101 runs off 120 balls in the 38th over when he was removed by paceman Ishant Sharma, who broke the 171-run fourth-wicket stand.
De Villiers went on to make 109 at faster than a run a ball, for his 16th career ton, before Umesh Yadav had him trapped leg before in the 44th over.
David Miller carried the lower order with a splendid knock, adding a quickfire 56 off only 34 deliveries.
Sharma was the pick of the Indian bowlers, bagging key wickets and picking up 4/40, while Mohammed Shami returned 3/69.
India will play a two-day tour match against an SA Invitation XI in Benoni on Friday andSaturday.
The first of two Tests will be played at the Wanderers next week.