Only six overs were possible before lunch, during which time the Proteas added 19 runs to their overnight total for the loss of Du Plessis.
The rest of the day was a washout as heavy rain kept the players from the field, meaning an earlier start on Sunday at 1000 local time (0800 GMT) to make up some of the lost overs.
"It's very frustrating for us," Du Plessis told reporters. "We are in a commanding position and what the rain does on a day like this is bring the opposition back into the game."
Du Plessis, 99 not out overnight, was made to wait another 90 minutes before play got underway and only faced two balls.
The first was a gift, a leg-stump half-volley from seamer Jerome Taylor that was easily dispatched to the square-leg boundary to bring up his century off 229 balls.
Taylor got it right on the second ball, though, finding a thin edge as Du Plessis looked to defend outside off stump and was caught behind by wicketkeeper Denesh Ramdin.
Hashim Amla will start day three on 23 along with AB de Villiers, who is nine not out, looking to accelerate.
West Indies will hope to break the partnership between the home side's two best batsmen quickly after they added a South African record of 308 for the fourth wicket in the first test in Pretoria.
The visitors will then try to run through the tail quickly with Stiaan van Zyl, playing his second game, and debutant Temba Bavuma the last remaining recognised batsmen.
Du Plessis said South Africa must speed up their scoring rate on day three.
"There is still some time left in the game," he added. "It means we are going to try and do whatever our plans were a lot quicker."South Africa won the first test by an innings and 220 runs. The third and final match of the series in Cape Town starts on Jan. 2.
(Editing by Ed Osmond)
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