Hyper-active Bafana Bafana (The Boys) shrugged off having a 78-second goal wrongly disallowed for offside to convincingly win a clash of teams missing club-tied Europe-based stars.
Bongani Zungu broke the deadlock on 31 minutes with a close-range shot and opportunist David Zulu doubled the lead after 53 minutes in the north-east city.
“South Africa were far too fast for us,” admitted Ivory Coast coach Herve Renard, the Frenchman who guided Zambia to a shock 2012 Africa Cup of Nations title.
“They were better in every area of the pitch and I counted only two scoring chances that we created.
“We were given a lesson and I hope my players learn from it as we prepare for the 2015 Cup of Nations in Equatorial Guinea.”
Success before a 15,000 crowd maintained the unbeaten record of Ephraim ‘Shakes’ Mashaba since being appointed Bafana coach last August.
He has overseen victories against Sudan (two), Congo Brazzaville and Ivory Coast, as well as draws with Nigeria (two) and Congo.
“I’m happy we maintained the momentum of recent months,” he said. “Fringe players were given a chance and some excelled.”
An experimental South African side quickly made their intentions clear as leading league scorer Puleng Tlolane netted with just over one minute gone.
But a flag was raised for offside and play continued while big-screen replays showed the Botswana assistant referee had erred.
South Africa controlled an opening half played at a fast pace and Zungu fired past Abdul Karim Cisse after slick, short passing created an opening.
And when substitute Ivorian goalkeeper Badra Ali Sangare dashed beyond his box to block a shot, Zulu pounced on the loose ball to net.
Sory Ibrahim Diomande had the best Ivorian chance 19 minutes from time, but his close-range shot lacked power and was pushed away by goalkeeper Jackson Mabokgwane.
The annual Challenge commemorates international icon Mandela, the first leader of a multiracial South Africa, who died aged 95 last December.