A minute later, Elise Bussaglia could have equalized from the penalty spot following a foul, but the Frenchwoman shot wide of the right post.
"They were an amazing team, but we had the most passion," Japan captain Aya Miyama said.
France attacked for the last 10 minutes of the match, with le Sommer coming close again with an overhead kick that was saved. Ogimi then the hit the post in the 90th after breaking from the halfway line.
Japan will play the United States in the final on Thursday.
Ogimi gave Japan the lead after France goalkeeper Sarah Bouhaddi fumbled an easy catch. The team's top scorer at the London Olympics got to the rebound first and bundled the ball in from close range.
Three minutes into the second half, Japan had doubled its lead when Sakaguchi looped a header into the top right corner.
"Today was even more disappointing than the World Cup," France coach Bruno Bini said. "In the last 20 minutes we played very well and were even better than Japan. They barely reached our side of the pitch."