India leads the five-Test series 2-0 after their second successive victory.
The home team had on Monday defeated South Africa 4-0.
The Indians scored late in both the halves through Chingelsana Singh (33rd minute) and Sandeep (68th), while Lance Louw (43rd) was the lone goal-getter for South Africa, at the Dhyan Chand National stadium.
The Indians, however, were far from impressive and looked scrappy throughout the 70 minutes' play.
As expected India coach Michael Nobbs made nine changes in the starting line-up and handed the captain's armband to Tushar Khandekar, who played his 200th international, in place of Sardara Singh, who was rested.
The changes seemed to have disturbed the home team's rhythm as the Indians looked rusty and out of sorts for most part of the opening period.