Olympic silver medallist Jonny Brownlee, who also won the silver medal behind elder brother and double Olympic champion Alistair at the 2014 Glasgow Games, finished seventh behind Schoeman.
Alistair was 10th as the brothers, who have been among the top contenders at global championships since 2011, faded badly on the run after they had led out a breakaway pack of six on the cycle leg of the sprint-distance event.
"It was pretty terrible today," Jonny said. "From start to finish I didn't feel great, I had ups and downs."
South Africa's Henri Schoeman poses with his country's flag after winning the mens triathlon final during the 2018 Gold Coast Commonwealth Games at the Southport Broadwater Parklands venue in Gold Coast
Image credit: Getty Images
Both brothers had been hampered by injury heading into the Games and Alistair, who carried the England flag during the opening ceremony, said a calf injury had restricted him from doing any serious training at all.
"I hadn't done enough to be fit enough on the run," he said.
"I knew it was going to be tough when you haven't actually run that fast for more than a minute or two at a time and, when you've got to do it for 15, it's not going to go very well for you.
"I would have preferred my calf to be good two months ago, if it was and I was able to train in that time, I reckon I would have been able to win that race."
Jonny added that he had an issue with his femur, which also restricted the amount of training he could do before the season began.
"I missed a lot of training but I thought I would do better than this," Jonny said.
"I dived in and felt pretty weak on the swim and ... started riding and I found it really hard to catch up. Then I started running and I thought, 'Oh dear, I'm in trouble here'.
"My first thought was 'I wish I was fit'. My body has let me down this year more than Alistair's."