Canada's Leah Kirchmann finished third, with Britain's Lizzie Armitstead colliding with France's Pauline Ferrard Prevot in the last kilometre and forcing her out of contention.
It was the first edition of the women's day race at the Tour de France. It took place ahead of the climax of the men's race, which was won by Vincenzo Nibali.
"It was already fantastic just to race here," said Vos. "That was a dream come true with the huge crowds.
"But it was also an incredible race with lots of attacks, and that makes it even better to win. The feeling is just amazing.
"I hope this got the attention that we all wished. I hope everybody feels the positive vibe that I feel now - that this is the start for more and lets have talks to grow the sport."
1. Marianne Vos (Rabo-Liv)
2. Kirsten Wild (Giant-Shimano)
3. Leah Kirchmann (Optum)
4. Lisa Brennauer (Specialized-Lululemon)
5. Shelley Olds (Ale Cipollini)
6. Coryn Rivera (United Healthcare)
7. Jolien D’Hoore (Lotto-Belisol)
8. Emma Johansson (Orica-AIS)
9. Simona Frapporti (Astana Be Pink)
10. Roxane Fournier (Poitou-Charantes Futuroscope)
- Sports & Recreation
- Lizzie Armitstead
- Leah Kirchmann
- Marianne Vos