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 8.35pm local time after an hour-long interruption.
Earlier India's bowlers were taken to the cleaners by Colin Ingram (78) and Jacques Kallis (61) as South Africa piled up an imposing total.
But Gautam Gambhir led India's riposte with a quickfire 49 off 28 balls.
The left-hander along with Robin Uthappa (18 off 19) added 71 runs 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 manage just seven runs, Gambhir slammed Albie Morkel for two boundaries and a six to put them on track.
There were a couple of quite 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 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.