The case concerns a 20-year-old marine who was swept away during flood relief work in July 2023, with reports saying he had not been given a life jacket.
Park Jung-hun investigated the incident for the military but was allegedly told to "hold off" on sending his report to police after he found a number of top military brass bore some responsibility for the accident.
At the time, the office of President Yoon -- currently suspended over his ill-fated attempt to declare martial law -- was accused by local media of involvement in the cover-up.
Yoon later vetoed lawmakers' efforts to set up a special investigation.
Park was accused of insubordination and dismissed from the military for allegedly transferring his findings to police, but the court acquitted him on Thursday, Yonhap reported.
The incident is regarded as a key event -- alongside the 2022 Itaewon crowd crush tragedy and first lady Kim Keon Hee's so-called Dior Bag bribery scandal -- that contributed to President Yoon's growing unpopularity.
Park, who was met with cheering supporters outside the court, thanked the military judges for their "wise and courageous decision".
He said the verdict was also a result of "the support, encouragement, and backing from the people" and vowed to continue his work to ensure justice for the late marine, Chae Su-geun.
The Military Court of Korea did not respond to AFP's request for comment.
Yoon has refused questioning and resisted arrest since his brief martial law decree on December 3 plunged South Korea into its worst political crisis in decades.
Investigators seeking to question the president on grounds of insurrection -- which is not covered by presidential immunity -- have a warrant to arrest Yoon, who is refusing to comply.
cdl/ceb/cwl
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