Two further wickets fell in Port Elizabeth as South Africa reached 369 for seven at lunch, scoring 80 runs in 23 overs during the morning.
With rain having washed out most of the second day's play, Amla looked keen to push the score along after yet more rain delayed Sunday's start by an hour.
The South African captain hit two fours in the first over of the day, bowled by Jerome Taylor.
New cap Temba Bavuma scored a boundary off his first ball, when a defensive shot flew to third man off a thick edge from Holder but De Villiers was out in the next over, bowled by Taylor.
De Villiers survived a failed review after a leg before appeal was turned down by umpire Paul Reiffel but was bowled next ball when he tried to work a full-length delivery to leg.
Van Zyl made 29 before he was caught behind, playing a loose drive against the left-armed Kenroy Peters.
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