The captain, whose name was not given, was convicted of breaking a clause in South Korea's military law banning homosexual activity by army personnel, the military said, adding it would continue to "handle disorderly conduct according to law."
He was sentenced to six months in prison, plus a suspended sentence of one year.
Homosexual acts are not a crime for civilians in South Korea, but it remains a conservative and patriarchal society and does not recognize same-sex marriage.
New President Moon Jae-In, elected earlier this month, is a former human rights lawyer and seen as a liberal, but came under fire from activists after saying in a televised debate that he did not like homosexuality.
Rights groups say that at least 32 soldiers face criminal punishment for similar actions.
"The captain was charged for having consensual sexual intercourse with his partner in a private space," said Kim Hyung-Nam of the Military Human Rights Centre campaign group.
Last month the organization accused the army of setting up fake accounts on dating apps to find military personnel and conducting homophobic interrogations on those exposed.
Rights group Amnesty International slammed the South Korean army for an "unjust conviction" that should be "immediately overturned".
"What counts is their service not their sexuality," said Roseann Rife, its East Asia research director.
"It is long overdue for South Korea to repeal this archaic and discriminatory provision in the military criminal code, and get up-to-date when it comes to the rights of lesbian, gay, bisexual, transsexual and intersex people," she added.
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source: news.abs-cbn.com
