The British rider started the day over two minutes down on race leader Julian Alaphilippe but chopped 29 seconds off the Frenchman's advantage after soloing clear of the bunch with 19 kilometres remaining.
The win was Yates' first since a stage in last year's Vuelta a Espana and he promised that there was more in the tank with two more mountain stages remaining in this year's 'Race to the Sun'.
"I started the day quite far down on GC, around two minutes," he told Cyclingnews as he jumped off the podium.
Yates's move came on the penultimate climb of the Col de Bourigaille and both Team Sky and Quick-Step Floors allowed the Orica rider a 15-second advantage by the time he crested the summit. The final climb into Fayence, with its average gradient of nearly 10 per cent, was still to come but Yates more than held on to take the win from Sergio Henao (Team Sky) at 17 seconds and Richie Porte (BMC Racing) at 26 seconds. The attack moved Yates up to eighth, 1:37 off Alaphilippe's lead.
"The climb where I attacked was quite short, so I knew that I wasn't going to take two minutes if I wanted to win the overall. I had to try something, and I'm just happy that it came off," Yates added.
"There weren't many riders left when I attacked, and the top of the climb came quite quickly. We reached the top so soon, and there was just one kilometre to go. I knew that it was now or never. Then it was a just a slog to the finish. The aim was the GC. I'm two minutes down, and I knew that it was going to be hard to bring back. I can only keep trying. Hopefully, I've got more to come."
When he arrived at his post-stage press conference, Yates admitted that Alaphilippe had the yellow jersey wrapped up, praising the Frenchman's talent having raced him since their junior days.
That said, Yates has proven himself to be in fine fettle, and stage 7 and 8 will provide further opportunities. At his post-stage press conference, Cyclingnews asked if his tactics for the remaining stages would change, given that he would be watched like a hawk after his stage winning antics.
"Maybe I'll be a bit more closely marked now," he said.
"I think that's one of the reasons today worked was because I was so far behind. There are a lot of guys who are closer and none of the guys were watching me today. Maybe tomorrow is a different story, and the day after, but we'll have to see. I'll give it a go and I can only hope for the best."
After Paris-Nice, Yates will step up his preparation for the Giro d'Italia, where he will co-lead Orica Scott alongside his brother, Adam.