Bafana Bafana made a great start, as Erick Mathoho headed in a Jabulani Shongwe corner eight minutes in for his first international goal.
However, the hosts equalised five minutes later when Erick Andino headed home after Itumeleng Khune palmed a curling strike on the angle by Carlos Discua into the winger's path.
Bafana coach Ephraim Mashaba took action soon after, hauling off left-back Mosa Lebusa - who struggled on his debut in the 1-0 win over Costa Rica last week - for veteran defender Clayton Daniels.
Mashaba was forced into another change midway through the first stanza following an injury to playmaker Thulani Serero. Bidvest Wits attacker Sibusiso Vilakazi made his entrance at the expense of the Ajax Amsterdam man.
Rubilio Castillo nearly put the home team in front around the half-hour mark, but his lob over the onrushing Khune was hacked away by Mathoho.
At the other end, Shongwe tested Noel Valladares with a useful shot shortly before the interval.
Neither side could make an impression in a physical second period, which saw Vilakazi hit the post late on.
Mashaba, who will have noted that Costa Rica beat USA 1-0 on Tuesday, also handed game-time to George Lebese, Bongani Zungu and Dean Furman.
The national team will be active again on Saturday in a CHAN qualifier with Angola at the Rand Stadium.
Honduras: Noel, Crisanto, Velásquez, Maynor, Oseguera, Mejía, Morazán, Martínez, Andino, Discua, Rubilio.
South Africa: Khune, Ngcongca, Coetzee, Mathoho, Lebusa (Daniels 16'), Jali, Mokotjo (Furman 70'), Masango, Serero (Vilakazi 24'), Shongwe (Lebese 56'), Patosi (Zungu 65').