The win is their first over the Bafana Bafana in seven previous clashes.
The scorer of the only goal of the game was Jonathan Kodjia when he connected home a well-calculated cross from Max Gradel in the 64th minute.
The game was an end to end affair, but Ivory Coast created most of the opportunities.
Kodjia missed an opportunity in the first half with just the goalkeeper to beat. He went for power and Ronwen Williams in post saved the situation with his strong hands.
The South Africa attack was virtually redundant throughout the game and their dangerman Tau failed to come to the party.
Bafana Bafana's only dangerous opportunity came in the early stage of the game, but it was denied by the woodwork.
Nicolas Pepe was a delight to watch with his runs, dribbles and set-pieces. In the first half his well-calculated free-kick hit the crossbar and in the second half Ronwen produced an acrobatic save to prevent another masterpiece free-kick from entering the net.
Wilfred Zaha’s place was taken by Kodjia and when he was introduced in the second half he added bite to the Ivorian attack.
Ivory Coast have atoned for their shambolic display in the last edition of the AFCON when they drew all their group games and exited in the group phase.