Japan went ahead on 32 minutes when Sarah Bouhaddi fluffed a catch from a long Aya Miyama free kick and the ball fell for Yuki Ogimi to scramble over the line.
It was 2-0 just 4 minutes after the restart and again from a free kick, this Mizuho Sakaguchi met perfectly with a header into the far corner with the keeper stranded, having taken a step the other way.
France immediately pressed for a way back into the game, Corine Franco blasted over after a corner then Marie-Laure Delie got away but Miho Fukumoto was out to block the shot.
Louisa Necib had a chance from 10 yards but Fukumoto got down very well to make the stop. But with 15 minutes left, Delie pulled the ball back and Eugenie Le Sommer was allowed to thump the ball home.
Just 3 minutes later, Le Sommer won a penalty for a foul by Sakaguchi but Elise Bussaglia placed the kick inches wide but with the keeper having dived the wrong way. Seconds later, France were in the box again as a frantic finale to the tie was brewing and although Le Sommer was on the ball, the keeper pounced.
Play switched to the other end and Homare Sawa almost caught Bouhaddi off her line, as she struggled to get back from an important clearance she had made. Ogimi then broke clear with a chance to seal the win but was denied by the post.
The game ended with an assault on the Japan goal, Wendie Renard's outstretched boot forced another great save in the dying seconds as the Nadeshiko managed to hold on to their narrow lead.
Japan will now be back at Wembley to face Canada or the USA in Thursday's final (KO 7.45), while France will contest the bronze medal match that afternoon at Coventry City FC, kick-off 1pm.
France: Bouhaddi, Renard, Georges, Soubeyrand (Abily, 56), Franco, Bompastor, Delie, Thomis, Necib, Bussaglia, Thiney (Le Sommer, 57).
Unused Subs - Deville, Boulleau, Meilleroux, Catala, Viguier.
Japan: Fukumoto, Kinga, Iwashimizu, Sameshima, Sakaguchi (Tanaka, 84), Miyama, Kawasumi, Sawa, Ohno (Ando, 74), Ogimi.
Unused Subs - Yano, Maruyama, Takase, Iwabucki, Kaihori.
Pictured - Yuki Ogimi forces home the opening goal for Japan. (Gavin Ellis/tgsphoto.co.uk)....more pics in the gallery.
She Kicks - the online news service for women's football