Andy Pycroft of the Emirates Elite Panel of ICC Match Referees imposed the fines after India were ruled to be three overs short of its target when time allowances were taken into consideration.
In accordance with the ICC Code of Conduct regulations governing minor over-rate offences, players are fined 10 per cent of their match fees for every over their side fails to bowl in the allotted time, with the captain fined double that amount.
"If Dhoni is found guilty of two further minor over-rate offences in Tests over the next 12 months, he will receive a one-match suspension as per the provisions of the ICC Code of Conduct," an ICC release said.
The penalty was accepted by Dhoni without contest so there was no need for a hearing.
The offence is contrary to Article 2.5.1 of the Code which relates to minor over-rate offences.
South Africa ended their second innings at 341 on the penultimate day yesterday.