The Court of Final Appeal ruled in favour of Angus Leung Chun-kwong, a senior immigration officer who took the government to court after being unequally treated by the city's biggest paymaster and the taxman, reports the South China Morning Post.
The ruling came just days after a separate case in which the Court of First Instance sided with a gay activist and struck down or revised seven criminal offences discriminatory against homosexual men.
Last year, the top court also backed an expatriate lesbian in recognizing her overseas marriage for the purpose of getting a spousal visa.
In a summarized judgment, the top court, which reached the decision unanimously, said it accepted the government had a legitimate aim to protect the institution of marriage.
Leung, 39, took the government to court in late 2015 after the secretary for the civil service refused to grant spousal benefits to his British husband, Scott Adams, the South China Morning Post said.
The couple, who are fighting for medical and dental benefits, married in New Zealand in 2014.
Leung also challenged the Inland Revenue Department for not allowing him to make a joint tax assessment with Adams, as heterosexual couples can do.
While Taiwan became the first place in Asia to allow same-sex marriage last month, Hong Kong's definition of marriage - between a man and a woman to the exclusion of others - has remained unchanged in the Marriage Ordinance since the 1930s.
( With inputs from IANS )