The Ivorians missed several key Euro-based players
Keiji Tamada's superb first-half volley gave Japan a 1-0 home victory over Ivory Coast in a friendly on Saturday.
Yoshito Okubo was guilty of a bad miss early on before Tamada showed his strike partner the way, sliding in to fire home a right-wing cross from Makoto Hasebe in the 21st minute.
Japan meet Paraguay in the final game of the three-nation Kirin Cup in Saitama on Tuesday.
Ivory Coast and Paraguay drew 1-1 on Thursday.
All three sides are warming up for World Cup qualifying matches next month, although Ivory Coast and Paraguay are missing key players who did not make the trip to Japan.
Ivory Coast begin their 2010 World Cup and Africa Cup of Nations qualifying campaign against Mozambique on 1 June, Botswana and Madagascar are the other two sides in Group 7.
English-based Emmanuel Eboue and Didier Zokora worked tirelessly for Ivory Coast but the Africans lacked a finishing touch in the absence of Chelsea pair Didier Drogba and Salomon Kalou.
Japan goalkeeper Seigo Narazaki was rarely troubled but reacted smartly on the hour to keep out a free kick from Etienne Boka which skidded through dangerously on the wet surface.
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