The 42-year-old ex-pro was unveiled as Cameroon manager in August, with fellow Dutch legend Patrick Kluivert as his assistant, but his first game in charge brought a sloppy performance.
The African Cup of Nations winners fell behind early on when El-Fardou Ben Mohamed put Comoros ahead in the 15th minute. The Red Star Belgrade striker tucked away a fine cross from Faiz Selemani to leave Andre Onana helpless in goal.
Playing on an artificial pitch at the Stade Said Mohamed Cheikh in Mitsamiouli, Cameroon struggled hard to find a response.
However, their efforts were rewarded in the 80th minute, when Angers striker Bahoken leveled the contest when he capitalized on some poor defending from Nadjim Abdou to score his first international goal.
Seedorf has yet to last more than six months in a club coaching role, despite jobs with AC Milan, Chinese side Shenzhen and Deportivo La Coruna.
Cameroon will defend their Nations Cup title on home soil in June next year, before targeting 2022 World Cup Qualification.