Honda, an Asian Cup winner with his country who also played for AC Milan, had previously said he would bring an end to his five-year tenure after the Games. In his swan song, the hosts came third in the five-team group after losses to Indonesia and Myanmar in the men's tournament, played by under-22 teams.
"A project in Cambodia that started in 2018 has ended," the 36-year-old former attacking midfielder wrote on Twitter, adding he "wasn't able to finish the last tournament with a satisfying result". The Cambodian football association also said it was "regretful".
Cambodia's SEA Games run started brightly with a 4-0 win over unfancied Timor-Leste. But a draw against the Philippines and two subsequent defeats meant they would not make the semi-finals. Because he lacked the requisite qualifications, Honda was never listed as official coach, but he led the team and was on the sidelines for matches.