“I was really going for that one,” said Wilde, who had a winning time of 1:42:13.
“I just wanted to do a bit better than Abu Dhabi [the last race of the series]. Unfortunately, that was mechanical and I didn’t get to show what I really had out there.
“So I wanted to come out here and really give it some.”
Australia’s Matthew Hauser was second, four seconds back from the Kiwi.
New Zealand’s Tayler Reid was 31st.
Wilde’s British rival and Olympic silver medallist Alex Yee was not at the Yokohama race, the second fixture of the 2023 WTCS calendar.
In the women’s race, Great Britain’s Sophie Coldwell claimed a breakthrough win.