The outcome could have been even worse for the 42-year-old ex-Real Madrid midfielder as his side fell behind after 15 minutes and levelled with only 10 minutes remaining.
Before succeeding Belgian Hugo Broos in June, Seedorf had unsuccessful spells as manager of AC Milan, Shenzhen and Deportivo la Coruna that lasted less than six months each.
He is being assisted by another former Dutch star, Patrick Kluivert, and ex-France international Jean Alain Boumsong is also part of the new coaching staff.
Reigning African champions Cameroon were ranked 47 in the world this month — 102 places above Comoros, a three-island state in southeastern Africa.
But the five-time Cup of Nations winners fell behind when El Fardou Ben Mohamed from Red Star Belgrade scored off a cross on an artificial Mitsamiouli pitch in humid conditions.
Cameroon often struggled to contain the islanders until Stephane Bahoken, who plays for French top-flight outfit Angers, equalised.
Guaranteed a place at the 24-team finals next June as hosts, Cameroon are playing in Group B with Comoros, Morocco and Malawi to gain competitive match practice.
Two nations qualify from each of 12 mini-leagues so the highest finisher between Comoros, Morocco and Malawi will accompany Cameroon to the biennial tournament.
A further 12 Cup of Nations qualifiers are scheduled for later Saturday.
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