France will play a third-place team on Sunday at Le Havre in the round of 16, and the victor will advance to a quarterfinal against the United States, Sweden or Spain.
Head coach of the Super Falcons, Thomas Dennerby, was an angry man, following their 1-0 defeat to France, in their final Group A fixture on Monday night.
Referee Melissa Borjas awarded a spot-kick after consulting VAR and adjudging that Viviane Asseyi had been taken down by Ngozi Ebere - who was shown a second yellow card for the challenge. Nigeria has played in every Women's World Cup but advanced past the group stage just once, reaching the quarterfinals in 1999.
Desiree Ellis' troops had a slim chance of advancing as one of the best third-place sides, although they needed Spain or China to lose in the other group B encounter.
But the referee ordered a replay, claiming that goalkeeper Chiamaka Nnadozie stepped off her line.
France had earlier beaten South Korea 4-0 and Norway 2-1, while Nigeria lost 0-3 to Norway and beat South Korea 2-0 in their second match.
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Renard hit the lower bar but Nnadozie was penalized for going off her line in the 76th minute before she kicked the ball from the spot.
Things were to go from bad to worse for Banyana as Dlamini gifted Germany with a second goal in the 29th minute.
"We wanted to win our three group games and it's done even if it was hard", said France coach Corinne Diacre.
After a nervy win over Nigeria, France will be aiming to rely on their support to push them all the way to World Cup glory.
- The hosts of a Women's World Cup tournament have won their final group stage match in the competition on seven occasions (W7 D1), with Canada in 2015 the only one of the eight sides not to win.