De Villiers reached his 21st test century in 144 balls and accelerated the scoring through the second session as South Africa sought to build an advantage on a batting track that showed signs of playing up with two days left.
A regular fall of wickets meant the hosts were unable to build a bigger lead, losing seven wickets after resuming on their overnight tally of 227 for three in reply West Indies' first innings tally of 329.
De Villiers was the last man out, caught on the boundary off spinner Marlon Samuels as he attempted to plunder the bowling in a final wicket partnership with tailender Morne Morkel (four not out).
De Villiers began the day 32 not out and sought to build some early momentum with Hashim Amla before the South African captain was caught behind by wicket-keeper Denesh Ramdin for 63 off the bowling of Jason Holder in an important breakthrough for the tourists.
Amla lost his wicket immediately after a brief delay for a change of the ball, which had gone out of shape after 75 overs and was deemed no longer usable by the umpires.
He was followed back to the dressing room by Temba Bavuma, bowled by Shannon Gabriel for 15, before de Villiers and Stiaan van Zyl put on a 96-run partnership for the sixth wicket.
Van Zyl, who survived a leg before wicket decision after a review, was eventually trapped by Samuels for 33.
Debutant Simon Harmer also survived a review as he made 10, his knock sandwiched between run outs for both Vernon Philander and Dale Steyn, both of of whom did not trouble the scorers.
A series victory for South Africa will see them retain their ranking as the top test-playing nation.
They won the first test in Pretoria by an innings and 220 runs but drew with the West Indies in the second test in Port Elizabeth in a rain-affected game.
(Editing by Pritha Sarkar)
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