Holder made 54 not out with six fours and one six and shared a key last-wicket partnership of 40 with Shamar Joseph (25).
West Indies resumed on their overnight score of 97-7 in reply to the Proteas’s 160 all out after an opening day which saw 17 wickets fall.
Medium pacer Wiann Mulder took 4-32 for SA with fast bowler Nandre Burger claiming 3-49.