Christiaan Jonker 49 off 24-ball is vain, India won final match by seven runs, and win series by 2-1.
The series is keenly balanced at 1-1 ahead of the final match of the tour in Cape Town on Saturday.
Fifties from JP Duminy and Heinrich Klaasen helped South Africa defeat India by six wickets in Centurion to level the three-match T20 series 1-1.
The hosts have to dig deep to level the three-match T20I series as they face India at Centurion on Wednesday.
India captain becomes only the second batsman to cross the 900-point mark concurrently in Tests and ODIs.
Dhawan struck 72 from 39 balls and Bhuvneshwar took a maiden five-wicket haul in T20Is to give India a convincing win over South Africa in Johannesburg.
India dominated the ODI series and appear favourites for the T20I series with the home side missing a host of first-choice players.
Virat Kohli breaks another record as India beat South Africa by eight wickets and lifting the series 5-1.
India will aim to continue their dominance to finish with a 5-1 record against the Proteas in ODI on Friday.
Even if South Africa wins on Friday, India will remain No.1 on 121 points, as cut-off date 1st April.