Kim Woo-jin won the all-Korean contest 6-4 for his third Asian Games gold but refused to celebrate his victory over compatriot Lee Woo-seok.
Korean law states that every able-bodied man must report for national service for 21 months before their 28th birthday, while exemption is offered to all Olympic medallists or Asian Games champions.
Kim secured his exemption eight years ago when he won two golds in the 2010 Games in Guangzhou. But for Lee, already serving in the armed forces, Tuesday's final was the last opportunity to win a gold and obtain an early discharge.
Kim said he performed without thinking about the implications of the outcome.
"It was just tough to beat someone that I know so well after months of training together," he was quoted as saying by Yonhap news agency.
Lee, who won a team silver on Monday, rued his performance.
"I am disappointed with the result, but I have to accept these results because they're all my own doing," he said.
"And the military isn't all that bad. South Korean men all have to go, anyway. I'll go back and serve the country the best I can."
Korean fencer and former Olympic gold medallist Gu Bon-gil did not rejoice after beating Oh Sang-uk in the men's individual sabre final last week.
Gu said he felt bad for his compatriot but South Korea subsequently won the team event, Lee's first Asiad gold.
The South Korean football team, who meet Vietnam in Wednesday's semi-finals, are two wins away from a successful title defence which would bring similar joy to Son.
(Reporting by Amlan Chakraborty; editing by Ed Osmond)
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