South Africa had already wrapped up the three-match series going into the final fixture on Saturday, when the threat of lightning on the Highveld shortened the contest.
South Africa won the toss and sent the tourists into bat for the third time in the series, with Hetmyer and opener Shai Hope (48 from 25 balls) helping the West Indies to 114 for three in their 10 overs.
The target for the home side was adjusted to 125 via the Duckworth-Lewis-Stern method, but the West Indies applied early pressure through their spinners.
Akeal Hosein (1-25) and Gudakesh Motie (3-17) put the home side on the back foot and as the rate grew, they lost wickets at regular intervals.
South Africa needed 16 off the last over from Shamar Joseph, who bowled a succession of yorkers to close out the game for the visitors.
"Five overs of powerplay and then basically five overs of death. They played some good shots and got a good score," South Africa captain Aiden Markram said. "We backed ourselves but fell short. It was a good exercise and there was definitely some good stuff to take home tonight.
"It was a good series with lots of good signs from us. The players are in good form. It is a nice thing to have going to the World Cup. Exciting times ahead and happy with where the team is at. We have got all bases covered."
Both countries now head to the T20 World Cup where the West Indies start against Scotland on February 7, while South Africa's first match is against Canada on February 9.
