Cousin (Direct Energie) finished ahead of breakaway partner Nils Politt (Katusha-Alpecin) and Andre Greipel (Lotto Soul) at the end of the 165km stage from Salon-de-Provence to Sisteron.
His win was the second for Direct Energie at Paris-Nice coming after Jonathan Hivert's Tuesday victory at Chatel-Guyon.
"I had cramps towards the end," Cousin said. "The goal was to go for the breakaway and take the KOM jersey. I did not spare my efforts and we had a tacit agreement that if I went for the climbers they would leave me alone on the flat.
"Now when I saw that the victory was possible I worked hard to go after the Katusha rider and I played with him a little. That's the way I won.
"I'm so generous in my efforts all year and I was beaten in similar circumstances so many times before that I decided to manoeuvre differently for once and see if it worked.
"I didn't rob this. Last year I raced for only thirty days. It's a great comeback.
"We now won two stages, It's important for the team but I must recover because I'm also supposed to be helping Lilian Calmejane make it into the top 10."
Astana's Luis Leon Sanchez continues to lead the race ahead of Wout Poels (Sky) and Julian Alaphillipe (Quick-Step Floors).
The Stage 6 198km run to Vence, which includes five climbs, is set to shake up the general classification.