Taking place in soaring temperatures and high humidity, the 23-year-old Loughborough-based athlete led for much of the 10km run before eventual gold medallist Kristian Blummenfelt (Norway) pulled away.
Making his Olympic debut in Japan, Yee looked in fine fettle throughout despite the Olympic final being just the eighth race he has competed in at this level.
The race started at 06:30am local time to avoid the worst of the heat and humidity but had to be restarted as a boat bizarrely blocked about half of the athletes from leaving the pontoon.
“[It's] amazing to feel I’ve fulfilled that dream," Yee told Eurosport.
"I just kept ticking away. I’m just an ordinary person and anyone can do this if you believe in yourself and keep ticking away.
"I hope I can serve as inspiration that anything is possible. Believe in yourself.”
Yee will also be performing in the mixed relay on Saturday which may also feature Loughborough University alumna Vicky Holland.
Loughborough’s dedicated 2020 Tokyo Olympic and Paralympic Games website features all the latest news, videos, and medal tables from Japan.