Dean Elgar made 199 and Hashim Amla scored 137 as South Africa batted remorselessly until tea before captain Faf du Plessis declared.
West Indian troubles did not end with the missed chances. Benn left the field after falling heavily while fielding.
Australia go from 152/1 to 216 all out to lose PE Test in final over of Sunday, a day before a wash-out was forecast.
Reduced to 11/2, South Africa indebted to two big stands forged by Elgar to take side to 214/5 by stumps on Day 1.
India A had won the first ‘Test’ by an innings and 13 runs at Rustenburg.
Englands bowlers dismissed South Africa for 211 in 46.4 overs in the third one-day international at The Oval on Friday.