South Africa were 270 for two at the close after being sent in to bat in overcast conditions at St George's Park.
Elgar made a Test-best 121 and shared a second wicket partnership of 179 with Du Plessis, who finished the day on 99 not out.
The West Indies missed four chances to break the Elgar-Du Plessis stand. The West Indian bowlers could feel aggrieved as they bowled with much better control and discipline than they did in Centurion where they were heavily beaten by an innings and 220 runs in the first Test.
One ball after Du Plessis' second escape, the left-handed Elgar went down the wicket to Benn and was well out of his ground as the ball squeezed through to hit low on the pad of captain and wicketkeeper Denesh Ramdin.
Elgar was on 48 and to add insult to the disappointed bowler he went down the wicket again and lofted Benn to the straight boundary to raise his fifty.
Holder was prevented from bowling in Benn's place in the next over because he had not been on the field long enough after being treated for a hand injury. Instead Taylor had to fill in at a time when he would have expected to be resting up ahead of taking the second new ball.
The left-handed Elgar made his third Test century - and his second at St George's Park - where he has now scored 323 runs in three Tests at an average of 107.66 compared to 362 runs at 22.62 in 11 appearances at other venues.
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