Chasing South Africa's 219 for four, India were fairly well-placed at 71 for no loss in 7.5 overs, 11 runs behind the par score under the D/L method, when the heavens opened up.
The match was called off at 8.35 pm local time after an hour-long interruption.
Earlier, India's bowlers were taken to the cleaners by Colin Ingram (78) and Jacques Kallis [ Images ] (61) as South Africa piled up an imposing total.
But Gautam Gambhir [ Images ] led India's riposte with a quickfire 49 off 28 balls.
The left-hander, along with Robin Uthappa [ Images ] (18), added 71 runs for the first wicket in no time, keeping India in the hunt for a stunning win at the New Wanderers.
After a rather quiet first over, in which India could score just seven runs, Gambhir slammed Albie Morkel [ Images ] for two boundaries and a six to put them on track.
There were a couple of quiet overs after that, but Gambhir's aggressive approach at the crease kept the South African bowlers at bay.
However, as it turned out, it was not the most appropriate end to a match whose proceeds will be going to charity, for the Jacques Kallis Foundation.
Apart from charity, the match was organised to celebrate 150 years of settlement of Indians in South Africa.
Earlier, electing to bowl, Mahendra Singh Dhoni's [ Images ] men found themselves at the receiving end of the Proteas' onslaught as Ingram and Kallis added 119 runs for the second wicket in just 13.2 overs.
Albie Morkel led with a three-ball 16 to provide the late flourish while Justin Ontong slammed 22 off seven balls.
So harsh was the onslaught that South Africa were past the 100 mark by the 12th over, with the 200 coming in the last over of the innings, bowled by Suresh Raina [ Images ], thanks to some prolonged power hitting.
Pathan fought back with the wicket of Levi, inducing the batsman to offer an outside edge to first slip.
The setback, though, had no effect on the South Africans, who rode on Kallis and Ingram's big hitting to put the Indians on the backfoot.
While the big shots came in a barrage, the one that stood out early on was Kallis's towering six off Yusuf Pathan [ Images ].
The off-spinner, who was preferred over Ravindra Jadeja [ Images ], tossed one up for Kallis, who took a few paces forward to loft it over long-on.
Ingram was not far behind, matching his senior partner stroke for stroke.
The left-hander swung Ashwin over deep midwicket for a huge six after the bowler dropped it a fraction short.
It was then Rohit Sharma's [ Images ] turn to taste the music as Kallis rocked back to hit the part-time spinner delivery back over deep midwicket for the maximum.
South Africa handed debuts to Farhaan Behardian and Dane Vilas.