South Africa came into the second day 270-2 following Dean Elgar's impressive 121-run knock, but could only add 19 runs to their haul in Port Elizabeth.
Rain had delayed the opening session by two hours, but Faf du Plessis - on 99 not out overnight - managed to bring up his century with a four off the first ball of the day.
However, Du Plessis's innings was over with the very next ball when he was caught behind off Jerome Taylor.
Umpire Paul Reiffel had initially ruled it not out, but the Snickometer revealed a slight nick on the outside edge.
Hashim Amla (23 not out) and AB de Villiers (9) were just beginning to hit their stride when the rain returned, forcing an early lunch.
Despite attempts to ready the pitch for a restart, stumps were called for the day, leaving South Africa 289-3.