Opener Smriti Mandhana (84 off 98) scored a strokeful fifty while pace duo of Jhulan Goswami (4/24) and Shikha Pandey (3/23) shared seven wickets between them to emerge as the architects of India's victory.
Electing to bat, left-handed batswoman Mandhana hit eight boundaries and a six in her 98-ball innings and shared a 99- run stand with skipper Mithali Raj (45) to help India post 213 for seven in their allotted 50 overs.
Pandey rocked the hosts early by removing opener Lizelle Lee (3), wicket-keeper Trisha Chetty (5) and Mignon du Preez (0) to leave them at 23/3 in 9.2 overs.
Spinner Poonam Yadav (2/22) then accounted for the other opener Laura Wolvaardt (21), while Goswami trapped Chloe Tryon LBW as South Africa lost half their side in 22.5 overs.
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Marizanne Kapp (23) and Niekerk tried to resurrect the run chase but Yadav sent the former back to the hut and left- arm spinner Rajeshwari Gayakwad removed the home side skipper after they reached the 100-mark.
Earlier electing to bat, India lost their first wicket when Ayabonga Khaka dismissed opener Punam Raut (19) with Shabnim Ismail taking the catch. Mandhana and Raj then steadied the ship before the opener was removed by Khaka with Sune Luus taking the catch.
Next over, Masabata Klaas got rid of Raj as India slipped to 155/3 in 36.1 overs. South Africa then effected two run outs, dismissing V Krishnamurthy (2) and DB Sharma (6) to further reduce the visitors to 168-5 in 42 overs.
Brief Score:
India women's team: 213 for 7 in 50 overs (S Mandhana 84; M Kapp 2/26)
South Africa women's team: 125 all out in 43.2 overs (D van Niekerk 41; Jhulan Goswami 4/24).