Keshav Maharaj (L) and Rishabh Pant pose for pictures as they share the trophy after rains interupted the final T2 at the at the M. Chinnaswamy Stadium in Bangalore on Sunday. AFP
The hosts bounced back from 2-0 down to level the series with convincing victories in the absence of top stars including regular captain Rohit Sharma and batting stalwart Virat Kohli.
Rain played spoilsport in the series decider in Bangalore when persistent showers forced umpires to call off the match with just 3.3 overs bowled and India on 28-3 after being put into bat first.
"It might get a little bit frustrating (with the no result), but there are a lot of positives, especially the way the whole team showed character after the series was 2-0 (in favour of South Africa)," said Pant.
Bhuvneshwar Kumar receives Man of the Series trophy. AFP
"We are just finding different ways to win the matches, we are trying to play different kind of cricket which we never used to play. There will be mistakes but as along we learn from our mistakes and keep improving it will be fine."
India won the third match by 48 runs and then hammered the hosts by 82 runs for their second successive win on Friday.
Pace bowler Bhuvenshwar Kumar was named player of the series for his six wickets. Indian opener Ishan Kishan topped the batting chart with 206 runs.
Pant, who was made national captain for the first time ahead of the series when KL Rahul pulled out injured, had an ordinary outing with scores of 29, 5, 6 and 17.
"It is for you guys to decide on how I am doing as a player and captain," the wicketkeeper-batsman said on his first series as Indian leader. "I can only focus on giving my 100 per cent every time I go on the field and keep improving."
India now head to Ireland for two T20 matches while a few players including Pant head straight to England for a rescheduled fifth Test starting July 1 in Birmingham.
In the final T20, play started 50 minutes late, when rain forced the teams to head off the field just before the first ball was bowled.
South African quick Lungi Ngidi bowled the left-handed Kishan for 15, and then got his opening partner Ruturaj Gaikwad caught at mid-on for 10.
Shreyas Iyer, on nought, and skipper Rishabh Pant, on one, were batting when play stopped for second the final time.
Earlier, South Africa skipper Temba Bavuma was ruled out of the line-up due to an elbow injury he suffered in the team's previous loss. Keshav Maharaj stood in as captain.
"We're a work in progress, and we're trying different combinations to see how we shape up ahead of the (T20) World Cup," said Maharaj.
Needing 149 for victory on a hot and humid day in Cuttack, South Africa rode Klaasen's fourth T20 half-century to achieve their target in 18.2 overs and lead the five-match series 2-0.
The hosts were chasing a target of 177 to finish the series on a high after going down miserably against the visitors in the first two matches. Shanaka scored an unbeaten 54 off 25 balls with five fours and four sixes to seal a four-wicket victory.
Though Babar scored a half-century and Pakistan won the low-scoring warm-up game against the West Indies on Monday, the captain consumed 41 deliveries for his 50, while Rizwan struck his 13 off 17 balls and didn't score a single boundary.
Namibia reached the Twenty20 World Cup second round for the first time on Friday when they defeated Ireland by eight wickets.World number 19 Namibia, the lowest-ranked team in the tournament, chased down their modest target of 126 with skipper Gerhard Erasmus making an unbeaten 53.
In another dominant performance, UAE defeated hosts Malaysia by five wickets in the final of the ACC Women’s T20 Championship on Saturday.
Petra Kvitova warmed up for Wimbledon by winning the Eastbourne singles title for the first time with a 6-3, 6-2 rout of Jelena Ostapenko on Saturday.
A 13.2km time trial will get the 109th edition of the Tour De France underway, before the riders eventually roll into the mountains and push their bodies and physical capabilities to the absolute limit.