South Africa were 340 for three at the close. Amla, captaining South Africa for the first time in a home Test, made 133 not out, while De Villiers hit an unbeaten 141. They added 283 for the fourth wicket, a South African record against the West Indies.
The pair came together with South Africa in a minor crisis after losing three wickets for no runs with the total on 57.
Much of the bowling was mediocre and the tourists suffered a blow when Kemar Roach, who was comfortably their best bowler, pulled up lame after bowling five balls of his 16th over half an hour after tea.
Roach was surprisingly not given the new ball and runs flowed freely from South African openers Alviro Petersen and Dean Elgar before Roach was brought into the attack after nine overs.
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Roach's wickets sandwiched the dismissal of Elgar, who was caught at gully off left-armer Sheldon Cottrell. The three wickets fell in the space of 15 balls.
Rain delayed the start by half an hour and the sky was overcast for almost the entire day but with the exception of Roach, the bowlers were not consistent enough to exploit any assistance from the conditions.