In reply, Lizelle Lee score an unbeaten hundred (131-ball 132) before rain stopped play in the 47th over with South Africa 223 for 4, six runs ahead on the D/L par score.
For India, Julan Goswami (2/20) was the pick of the bowlers while Rajeshwari Gayakwad (1/39) and Deepti Sharma (1/39) scalped a wicket each.
The two teams will now face each other on Sunday in the fourth ODI at the same venue.
India women: 248 for 5 in 50 overs (Punam Raut 77, Deepti Sharma 36 not out Mithali Raj 36, Harmanpreet Kaur 36; Shabnim Ismail 2/46)
South Africa women: 223 for 4 in 46.3 overs (Lizelle Lee 132 not out; Mignon du Preez 37; Julan Goswami (2/20) (UNI)