But van der Dussen made an unbeaten 75 and shared a vital 70-run partnership for the eighth wicket with Kagiso Rabada, who made 40 from 48 balls, to diminish the home team's chances.
South Africa was finally out for 174, building its lead to 323 which may be beyond the reach of the West Indies whose best total of the series so far is 162.
Openers Kraigg Brathwaite (5 not out) and Kieran Powell (9 not out) batted out the last six overs of the day in fading light to guide the West Indies to 15 without loss at stumps when they still trailed by 309.
The task of chasing that total in the fourth innings is difficult on a wearing pitch, especially for a West Indies team whose batsmen have struggled throughout the series. The home side might also be without Roston Chase who has a leg injury.
But Brathwaite will take heart from the memory of the West Indies' successful chase for a similar total against England at Headingley in 2017, when he scored 134 in the fourth innings.
Van der Dussen showed Sunday that runs can be scored with application. He batted through more than 40 overs to steady the Proteas' innings.
"I was a bit of a hiccup at the start of our innings," van der Dussen said.
"But we came into the day knowing that we were on the front foot and we wanted to play like we're on the front foot.