The two teams will next meet on Sunday in the fourth ODI.
The Indian women's team suffered a six-run loss to South Africa via the Duckworth/Lewis method in the third ODI here on Friday.
Put in to bat, Punam Raut starred for the home team with a 108-ball 77, which was studded with 11 boundaries. India scored 248 for five in the allotted 50 overs.
In reply, Lee struck a 131-ball unbeaten 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, veteran pacer Julan Goswami (2/2O) was the pick of the bowlers while Rajeshwari Gayakwad (1/39) and Deepti Sharma (1/39) picked a wicket each.
This is India's highest ever first innings total in a home ODI that has resulted in a defeat.
India now trail the five-match series 1-2.
The two teams will next meet on Sunday in the fourth ODI.
Brief Scores:
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)
