The Proteas' woes were compounded after their defeat to New Zealand on Saturday, when they lost the services of captain AB de Villiers for the rest of the series, along with their status as the top-ranked ODI team in the world.
De Villiers was suspended for two ODIs and his players forfeited their entire match fee as a penalty for the slow over-rate in the one wicket loss in Paarl.
Match referee David Boon ruled that the hosts were six overs short of their target at the end of the match when time allowances were taken into consideration.
The South African captain pleaded guilty, so no hearing was necessary.
The teams meet again in the second of three ODIs in Kimberley tomorrow and Faf du Plessis now assumes the captaincy.