The Proteas scored 195-3 after being put in to bat and David Wiese then took 5-23 as they restricted the tourists to 126 all out and claimed a convincing consolation victory, the West Indies having already clinched the series.
West Indies opener Chris Gayle was man of the match in the first two games but sat this one out with a back injury while South Africa rested captain Faf du Plessis ahead of the upcoming one-day international series.
Justin Ontong led the South African team but was not required to bat as Van Wyk produced a superb knock.
The 35-year-old, who has been recalled to the team because of an injury to Quinton de Kock, smashed 114 not out off 70 balls with seven sixes and nine fours.
Van Wyk and Reeza Hendricks (42) got the innings off to a rousing start with an opening stand of 111 in just under 13 overs.
David Wiese made 21 off 16 balls but the innings lost a bit of momentum during the latter overs and Rilee Rossouw was caught behind first ball.
However, having reacted jubilantly after reaching his ton off the second ball of the final over, Van Wyk celebrated in style with two sixes off Dwayne Bravo.
And JP Duminy (7 not out) also cleared the ropes as the final over of the innings went for 23.
The West Indies reply started well, Lendl Simmons doing a reasonable impression of Gayle as he hit 49 off 31 balls.
But it all started to go wrong when Dwayne Smith (5) was bowled by Aaron Phangiso with the first ball of the sixth over.
And medium-pacer Wiese then took a string of key wickets, having Marlon Samuels (6) caught by Ontong, before Simmons holed out to Duminy at long-on trying to hit his third six of the innings and Bravo (12) was caught behind.
At 84-5, Kieron Pollard (20 not out) was left facing mission impossible and Wiese???s great night continued as he removed Windies skipper Darren Sammy (8) and Carlos Brathwaite.
However, it was Marchant de Lange (2-26) who finished things off, hitting middle and leg to bowl Sheldon Cottrell for a golden duck to wrap up the victory.