"Pretty nice," Kooij told broadcaster Eurosport at the finish. "I won a few races last year. This is definitely the nicest so far."
The pack was all together as the longest stage of the race reached the finish in Saint-Paul-Trois-Chateaux.
Kooij, a 21-year-old who rides for the powerful Jumbo-Visma team, burst away from established sprinters Dane Mads Pedersen of Trek-Sagafredo and Belgian Tim Merlier of Soudal-Quick Step.
Pedersen had edged Kooij at the finish of the second stage.
"I was in the wheel of Pedersen and this time I was able to get out of his wheel," Kooij said. "Coming close and coming second is not bad but the victories are the ones that count."
As the sun finally came out, the pack of 148 rode the 212.4km stage at a languid pace.
"I enjoyed the first day in yellow. Really nice day and no stress," said Pogacar of Team UAE.
The Slovenian did burst into action briefly in an intermediate sprint for bonus seconds, finishing third to gain two seconds.
Frenchman David Gaudu of Groupama, in second place overall, edged Pogacar in the sprint with 57km to go to claim six seconds and cut the overall lead to six seconds.
"Only two today," said Pogacar with a laugh.
He increased his edge over reigning Tour de France champion Jonas Vingegaard, a Dane who also rides for Jumbo, to 46 seconds.
The race heads for the hills for the last three stages starting on Friday with a rolling 197.4km ride from Tourves to La Colle-sur-Loup.
