South Africa were 157 for one at tea after being sent in to bat in overcast conditions.
Dean Elgar (85 not out) and Faf du Plessis (42 not out) put on an unbeaten 110 for the second wicket but both should have been dismissed.
Du Plessis was put down by Marlon Samuels at gully off Jerome Taylor when he had made eight and again by Devon Smith diving to his right off left-arm spinner Suleiman Benn when he was on 26.
Elgar was on 48 and to add insult to injury for the disappointed bowler he went down the wicket again just after that and lofted Benn to the straight boundary to raise his fifty. Elgar could have been run out on 73.
After a mix-up with Du Plessis, he was several metres short of safety when Kenroy Peters' throw from midwicket missed the stumps at the bowler's end.
Petersen played a rash stroke against Shannon Gabriel and was caught by Leon Johnson, running back from cover.
Gabriel was one of three changes in the West Indian bowling line-up.
Gabriel, debutant Peters and all-rounder Jason Holder all bowled accurately in overcast conditions.
Gabriel and Holder were particularly effective in tandem, conceding only ten runs in nine overs after Petersen's dismissal. South Africa made two changes from the side that won the first Test at Centurion by an innings and 220 runs.
He replaced the injured Quinton de Kock and is the 85th player to be capped since South Africa returned to Test cricket in 1992.
A B de Villiers, who will continue to keep wicket as he did in both West Indies innings in the first Test after De Kock's injury, is playing in his 97th consecutive Test since his debut ten years ago.
By doing so he moved one ahead of Australia's Adam Gilchrist, the previous record-holder for most consecutive Tests from debut.
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