Match referee Andy Pycroft imposed the sanction after Temba Bavuma’s side was ruled to be one over short of the target after time allowances were taken into consideration.
“In accordance with Article 2.22 of the ICC Code of Conduct for Players and Player Support Personnel, which relates to minimum over-rate offences, players are fined 20 per cent of their match fee for every over their side fails to bowl in the allotted time,” the ICC said in a statement.
Bavuma pleaded guilty to the offence and accepted the proposed sanction, so there was no need for a formal hearing.
On-field umpires Marais Erasmus and Adrien Holdstock, third umpire Bongani Jele and fourth umpire Allauhudien Palekar levelled the charge after the match on Friday.
South Africa defeated India by seven wickets in the second ODI to take an unassailable 2-0 lead in the three-match series.
India made 287 for six after opting to bat. Rishabh Pant top scored for the visitors with 85 off 71 balls while skipper K L Rahul made 55 off 79 balls.
Spinner Tabraiz Shamsi was the pick of the South Africa bowlers, taking two wickets for 57 runs in nine overs.
South Africa chased down the target in 48.1 overs. Janneman Malan was the home team’s top-scorer with 91 off 108 while his senior opening partner Quinton de Kock made 78 in 66 balls.