The Trek-Segafredo rider was part of an elite group of six that pulled clear of the pack at the bottom of the Cote de Rimiez, 44km from the finishing line.
The elite group led by Annemiek Van Vleuten worked in unison and long-range attacks leading into the anticipated sprint finish from Van Vleuten and Deignan's team-mate Elisa Longo Borghini were shut down by Marianne Vos.
Longo Borghini then made another attack from the back of the group and Vos stayed on her wheel and looked the likely winner, but Deignan anticipated and sat in Vos' slipstream before making her decisive move, taking victory at the last moment with a bike throw on the finishing line.
The 31 year old said after her victory: "I was just relieved that I won it. What a performance by Trek-Segafredo today. Every single rider played their part and me and Elisa just really had to wait for final.
"Elisa did the perfect job, forced Marianne to sprint early and I took advantage of that. I think I had two of the best sprinters in the world in the car, Ina-Yoko Teutenberg and Giorgia Bronzini have both beaten Marianne Vos in lots of sprints so I had the best advice and their advice was 'patience' and I took it."
Deignan was relieved to see her hard work pay off with glory.
She added: "It's phenomenal! Sometimes when you're training hard and things aren't going your way it's frustrating and finally it seems like the luck is on our side. To be part of Trek-Segafredo is the best feeling and this is a team victory.
"It's really special. I know my husband and my daughter were watching on television and I can't wait to pick up the phone and speak to them."
Support The Yorkshire Post and become a subscriber today.
Your subscription will help us to continue to bring quality news to the people of Yorkshire. In return, you’ll see fewer ads on site, get free access to our app and receive exclusive members-only offers.
So, please - if you can - pay for our work. Just £5 per month is the starting point. If you think that which we are trying to achieve is worth more, you can pay us what you think we are worth. By doing so, you will be investing in something that is becoming increasingly rare. Independent journalism that cares less about right and left and more about right and wrong. Journalism you can trust.