The Proteas' woes were compounded after their defeat to New Zealand on Saturday, as 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 match fees as penalty for the slow over-rate in the first game 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.
De Villiers pleaded guilty so no hearing was necessary.
Selection convenor Andrew Hudson said vice-captain Hashim Amla asked not to be considered for the captaincy, so he could concentrate on his batting, and Faf du Plessis would skipper the side for the last two games of the series.
"Losing AB for the remainder of the series is obviously a big blow to us, particularly as he is still growing in the captaincy and needs every opportunity ahead of the ICC Champions Trophy in the middle of the year," Hudson said.
Cricket South Africa confirmed that Dolphins batsman David Miller had been called up as a replacement for De Villiers in the 14-man ODI squad.
The Proteas went down by one wicket in the series opener, after scoring just 208, a loss which cost them their number one ICC ranking. They are now third, with a rating of 116, behind India (119) and England (118).
"We should have lost by seven or eight wickets, so I am proud of the fightback in the field," De Villiers said.
"But overall, it was not good enough. We are operating at about 80 percent of our potential, but we are still trying to establish the team and get the team spirit we want.
"There are a lot of new faces, so there is still a lot of work to be done."
South Africa, batting first, were boosted by a fighting 57 from Faf du Plessis, who provided the anchor in stands of 46 with Colin Ingram and 59 with Ryan McLaren as they rebuilt from a position of three for 37 after 11 overs.
A whirlwind 26 off 20 balls from Rory Kleinveldt helped push the total over 200.
South Africa started well with the ball, taking three wickets for 21, but the New Zealand middle-order kept the scoreboard moving.
The Black Caps were also helped by the addition of 31 extras, including 15 wides and three no-balls, which De Villiers said was unacceptable.
"It is something we will have to work on before the next game," he said.
"That is not acceptable at this level." For New Zealand, man of the match James Franklin produced a solid innings of 47 off 61 balls with good support from Nathan McCullum (24) and Kyle Mills (26) which edged the tourists from a seemingly hopeless position of 105 for seven to an unlikely victory.
"It was just a case of digging deep and seeing how far we could take the game," Franklin said.
"I got tremendous support from Nathan and Kyle and they took a lot of pressure from me." Cricket South Africa and Eskom apologised for the power failure which hit Boland Park during the New Zealand innings and which prevented any referrals to the third umpire. Neither captain, however, believed it affected the outcome of the game.
The teams meet again in the second of three ODIs in Kimberley on Tuesday.