After a goalless 90 minutes, three goals were scored in extra time. His late header halved the deficit, but a Son-inspired South Korea held out for victory.
Son danced into the Japan penalty area early in the first period of extra-time and, as the forward prepared to pull the trigger, Verona forward Seung-Woo Lee swept in to rifle the ball into the top-left corner of the Japan net.
But whether it's gold or silver, the medal will go down in the history books as it will be the first medal won by a unified Korean team in ball sports at an worldwide multi-sports competition. The Defense Ministry has pledged to reduce the term to 18 months by 2020. But athletes are able to get exemptions by winning gold at the Asian Games.
South Korea beat neighbours North Korea to take gold in 2014 but Son was not in the squad as his club at the time - Bayer Leverkusen - exercised their right to refuse his release. Having been signed in 2015 for £22m, Son signed a five-year deal last July.
Tottenham forward Son Heung-min will get to skip military service.
He was thanked Tottenham for allowing him to play in Indonesia, where he captained South Korea. As an able-bodied man in his twenties, Son Heung Min would have had to serve in the military in the near future, had his team not won this gold medal.
In the past there has been tremendous public criticism of those, such as the children of government officials, who manage to find loopholes in order to avoid military service. He is still banned from entering South Korea.
Yoo Seung-jun, a popular singer in the 1990s, had to give up his career in South Korea after he was accused of evading military service by becoming a USA citizen.