Headers by Wilfried Bony and Gervinho just 98 seconds apart secured the win for the Africans, after Japan’s star Keisuke Honda put them ahead with an impressive 16th-minute strike.
“The players are very happy with the victory, but we are far from being qualified,” Lamouchi said.
“We only won one match. We have another tough game ahead [on Thursday] against the leaders of the group [Colombia]. We will have to prepare.”
The Elephants left captain Didier Drogba out of the starting line-up but his arrival off the bench after an hour coincided with Ivory Coast finally converting their chances, although the former Chelsea striker was not involved in either goal.
Swansea striker Bony equalised on 65 minutes with a glancing header, before former Arsenal forward Gervinho beat Eiji Kawashima at his near post to stun the Japanese.
Japan boss Alberto Zaccheroni remained confident his team could progress despite Saturday’s setback.
“We have to give credit to the Ivory Coast — they had a great game,” said the Italian, whose side continue their campaign against Greece on Thursday.
“We started well but could not hold onto the lead. The Ivory Coast players are very talented. We were not aggressive enough. We have to do better in order to reach the knockout round, because today we didn’t do enough.”
IVORY COAST: Barry, Aurier, Bamba, Zokora, Boka (Djakpa 75), Tiote, Yaya Toure, Die (Drogba 62), Gervinho, Bony (Konan 77), Kalou.
JAPAN: Kawashima, Uchida, Morishige, Yoshida, Nagatomo, Yamaguchi, Hasebe (Endo 53), Okazaki, Honda, Kagawa (Kakitani 86), Osako (Okubo 68).
Ref: Enrique Osses (Chile).