Wagner was sitting second behind 14-year-old Russian Julia Lipnitskaia, but she pulled away on day two and took the win with a final score of 190.63.
This was 11.01 points ahead of nearest challenger, Russia's Elizaveta Tuktamysheva, who leapfrogged compatriot Lipnitskaia who had to settle for third.
Great Britain's Jenna McCorkell at least ended on a high note in France as she lifted herself off the bottom in the free skate by two places to end the competition eighth.
In the men's competition Japan's Takahito Mura took his first figure skating Grand Prix title as he leapfrogged American Jeremy Abbot in the free skate.
The Japanese skater's score of 227.63 saw him edge out Abbott by 3.05 points, with former European champion Florent Amodio of France third in front of his home crowd with a score of 214.25.
Mura, who had never finished on the podium at a Grand Prix, denied former Grand Prix Finals winner Abbott his first win on the circuit since last year's Cup of China.
Home favourite and ex-world champion Brian Joubert had been third after Friday's short program, but a free skate score of 134.70 left him in fifth overall.
Amodio had been seventh overnight but surged back into contention by scoring 154.12 in the free skate, the day's best.
Russians Yuko Kavaguti and Alexander Smirnov claimed victory in the pairs despite finishing the free skate in second.
The 2010 European champions held the lead after the short programme and although Canadians Meagan Duhamel and Eric Radford put on the best show in the free skate it was not enough to overahaul Kavaguti and Smirnov.
The Russian duo took the win with 187.99 points, 1.18 ahead of Duhamel and Radford while Italians Stefania Berton and Ondrej Hotarek finished third.
And in the ice dance, European champions Nathalie Pechalat and Fabian Bourzat from France held on to their lead to claim the win.
They finished with a total score of 168.90, more than 15 points ahead of second-placed Anna Cappellini and Luca Lanotte from Italy, with Russians Ekaterina Riazanova and Ilia Tkachenko finishing third.
- Sports & Recreation
- Ice Skating
- Julia Lipnitskaia
- Takahito Mura