Luther Singh, Lyle Foster, Sipho Mbule and Mokoena, who missed the openig group game, were thrown straight into the starting line-up as the South Africans aimed for maximum points.
The South Africans made a strong start to the match when Mokoena lined up a long range shot from outside the box, but the SuperSport United man drilled the effort wide of the far post.
The Ivorians battled to withhold the pressure from the South Africans, as Foster scrambled a loose ball in the area ten minutes to halftime before going inches off target.
David Notoane ensured momentum remained with his charges during halftime and this was ratified with Kamohelo Mahlatsi on the charge early from the restart but the Ivorians cleared the threat.
A lovely turn inside the area from Foster 12 minutes from the break threatened the opener, but the Ivorians reacted sharply to avert the danger with a smart clearance.
A rare foray from the West Africans put the South Africans in a spot of bother on the hour mark before eventually clearing Junior Doumbia's delivery to maintain the balance of play.
Notoane's charges countered and found their dues on 79 minutes with a brilliantly taken free-kick from Mokoena which went in off the crossbar.
The South Africans pushed for a second later on, but Kodisang had his header cannoning off the crossbar in the final minute of the match as the encounter finished 1-0 in favour of the South Africans.