Schoeman covered the 1.5km swim, 40km ride and 10km run in 1:48:29, just three seconds behind third-placed Norwegian Kristian Blummenfelt after he was overtaken in the chase for the line.
It was his best performance of the year thus far on the top-flight circuit, after finishing 10th and eighth at the opening two legs of the campaign.
In the absence of compatriot Richard Murray, who skipped the Yokohama contest, former world junior champion Wian Sullwald battled through the rain to take 13th place in 1:50:11 as the only other SA athlete in the race.
Spaniard Mario Mola earned his second straight victory of the series in 1:48:15, climbing to the top of the world rankings.
Earlier, lone SA representative Gillian Sanders dropped out of the elite women’s race, with Flora Duffy of Bermuda taking the win in 1:56:18.
The fourth leg of the global series will be held in Leeds next month.