The Proteas had bulldozed their way through the Windies??? middle and lower-order on Monday, to leave their opponents 275-9 in their first innings and give themselves a faint hope of a victory.
But rain ??? a constant menace at St George???s Park over recent days ??? struck again overnight, drenching the playing surface and forcing umpires Billy Bowden and Paul Reiffel to curtail the match at 11am UK time.
South Africa won their opener with West Indies by an innings and 220 runs but now must wait until the third Test begins in Cape Town on Friday to try and wrap up a 10th Test series win in 12.
Port Elizabeth???s inclement weather allowed for just 201 of the scheduled 450 overs to be bowled in the second Test, with just six overs possible on day two as well as the zero on day five.
However, there was still time for four batsmen to score hundreds, with Dean Elgar (121) and Faf du Plessis (103) reaching that milestone for the hosts and Kraigg Brathwaite (106) and Marlon Samuels (101) following suit for the tourists.
Dale Steyn lit up St George???s Park either side of the lunch interval on day three, plundering 58 off 28 balls, including six fours and five sixes, as he posted the joint fourth fastest Test fifty in history and propelled South Africa to a score of 417-8 declared.
But the 31-year-old played second fiddle with the ball during West Indies??? knock, going wicketless while the height and bounce of Morne Morkel (4-69) and the spin of Imran Tahir (3-108) ripped through Denesh Ramdin???s visitors.
West Indies lost five wickets for 15 runs during a crazy end to day four but will take comfort from both the resolve they showed beforehand and the continued growth of Brathwaite, who has now scored three Test tons in 2014 and accrued an average of 77.88.
South Africa, meanwhile, handed a Test debut to Temba Bavuma in Port Elizabeth, making the right-hander the first black African batsman to play for The Proteas, plus AB de Villiers figured in his 97th straight Test from debut, overhauling the record of former Australia wicketkeeper Adam Gilchrist (96).