Before the winning goal, Wendie Renard's first attempt hit the outside post but the kick had to be retaken because Nigeria's Chiamaka Nnadozie had moved off her line -- a situation that also happened in France's previous game against Norway -- and the centre back coolly converted.
African champions Nigeria, who could still reach the last 16 as one of the best third-placed teams, finished with 10 players after Ngozi Ebere was sent off following a second yellow card in the 75th minute for a foul on Kadidiatou Diani that led to France's winning penalty.
The hosts France have now finished Group A nine points ahead of Norway with six and Nigeria on three, while South Korea have none. France will face one of the best third-placed teams in Le Havre on Sunday.
With Les Bleus having already booked a place in the last 16 before kick off, coach Corinne Diacre started Viviane Asseyi up front, with Eugenie Le Sommer starting on the bench.
France dominated possession in a packed Roazhon Park in Rennes, but were proving toothless up front, with their best chance coming midway through the first half when Amandine Henry's volley shaved the post.
Nigeria were looking to hurt Les Bleues on the break but the central defence, marshalled by Renard, kept the Super Eagles at bay.
The French were more aggressive in the second half, but Gaetane Thiney missed a sitter on the hour just before Le Sommer came on for Valerie Gauvin.
Just like in the 2-1 win against Norway, France were awarded a penalty after a Video Assisted Referee (VAR) review. Renard's first attempt hit the post but she made no mistake after the referee ordered the kick to be retaken because the keeper moved off her line.
Monday's game was France's eighth consecutive victory and their 17th in their last 18 outings.