South Africa batted out the remaining three overs of the day to reach four without loss in their second innings for an overall lead of 73, which at one stage looked certain to be considerably more.
Openers Dean Elgar (3 not out) and Aiden Markram (1 not out) will seek to extend that advantage on day three on a wicket that is still holding true for the batters.
West Indies looked as though they would trail South Africa’s first innings score of 320 by a substantial margin as the deficit stood at 127 when their last pair came together.
However, Holder led the charge with a superb display of counter-attacking stroke play, smashing four sixes and eight fours.
"It was good to get a partnership. The momentum was with us and I thought he (Motie) looked as comfortable as the top order batters," Holder told reporters.
"The most important thing was to stay in the game and we did that. We need some early wickets tomorrow morning. It's a pretty good pitch for batting."
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TOP SIX
Holder, who has a test double-hundred, believes he has the ability to bat in the top six in the West Indies side.
"I want to get up the order, I have had an indifferent time the last year, but I want to bat at six. I think I am good enough.
"I have worked really hard on a couple of things and today was an example of that."
South Africa started the day on 311-7 in their first innings but added only nine runs before being bowled out within 18 deliveries.
West Indies seamers Kyle Mayers (3-32) and Alzarri Joseph (3-60) along with spinner Motie (3-75) shared the wickets.
The visitors got off to the worst possible start in their reply as opener Tagenarine Chanderpaul was run out for one and they soon found themselves 28-3 as Kagiso Rabada picked up the key wicket of captain Kraigg Brathwaite for 17.
A few batters got starts, but they were rattled at 162-8 and it seemed only a matter of time before they would fold.
That was before Holder and Motie put on the biggest partnership of the innings, which eventually ended when spinner Simon Harmer had the latter caught at short cover for 17.
Seamer Gerald Coetzee was the pick of the home attack as he recorded figures of 3-41.
