Suryakumar Yadav and Rinku Singh hit rapid half-centuries for India but South Africa chased down an adjusted target to win the second Twenty20 international by five wickets at St George's Park in Gqeberha on Tuesday.
India, sent in to bat, were 180 for seven when rain ended the innings with three balls remaining in their 20 overs.
After a delay of almost an hour, South Africa were set to make 152 off 15 overs.
Led by a hard-hit 49 off 27 balls by opening batsman Reeza Hendricks, South Africa won with seven balls to spare. They took a 1-0 lead in the three-match series after the first match in Durban was rained off.
South African captain Aiden Markram admitted that the conditions favoured his team. Rain fell in the lead-up to the match before returning at the end of the Indian innings.
"The second bit of rain helped us. The ball skidded on a bit and also affected the outfield," said Markram.
Indian captain Suryakumar hit 56 off 36 balls and Singh was unbeaten with a career-best 68 off 39 deliveries.
Suryakumar went out to bat with the total on six for two after two overs. Both openers, Yashavi Jaiswal and Shubman Gill, were dismissed without scoring.
The precarious situation did not deter the captain and Tilak Varma (29) from going on the attack against some erratic bowling. They added 49 off 25 balls.
Suryakumar and Singh then put on 70 off 49 balls.
"That's the brand of cricket we want to play, whatever the situation," said Suryakumar.
Markram said the Indian assault meant he had to be strategic with the way he handled the bowlers, with player of the match Tabraiz Shamsi bowling his left-arm wrist spin in three spells to take one for 18, easily the most economical figures of the match.
"Shammy bowled incredibly well," said Markham.
Gerald Coetzee took three for 32, taking wickets with what proved to be the last two balls of the Indian innings.
Mohammed Siraj was walking out to face the hat-trick delivery when the umpires took the players off the field.
Brief scores:
India 180-7 in 19.3 overs (S. Yadav 56, R. Singh 68 not out; G. Coetzee 3-32).
South Africa 154-5 in 13.5 overs (R. Hendricks 49, A. Markram 30; M. Kumar 2-34).
Result: South Africa won by five wickets (DLS Method).
Series: South Africa lead the three-match series 1-0.