Visma's Jonas Vingegaard was second, doggedly staying right on Pogacar's wheel to the line with Briton Oscar Onley third after a late nine-rider pile-up marred the finale.
On his 19th career Tour de France stage win, the 26-year-old Pogacar gained four seconds on Vingegaard with ten bonus seconds to the Dane's six.
"It was super-hot today, and super fast, but we had a plan and we stuck to it," said the Team UAE rider who was champion in 2021, 2022 and 2024.
In the overall standings, Remco Evenepoel is second, 54 seconds off first as he came sixth on the day, two seconds adrift.
"The Tour de France isn't over yet," said Evenepoel, who lost time in a crosswind on stage one before winning the stage five individual time-trial.
French starlet Kevin Vauquelin continues his bright run in third at one minute, 11 seconds, while two-time champion Vingegaard is fourth at one minute, 17.
Fans cheered for Vauquelin along much of the route. On Thursday, a hot-air balloon flew over the peloton with his face on it.
"All you could hear was 'Kevin, Kevin' all along the road, it's so good to have a new face competing with us," said Pogacar.
The overnight leader, Mathieu van der Poel, rounds out the top five at one minute, 29 seconds, after wilting on the final climb, scene of his 2021 coming-of-age win and his first yellow jersey.
"I kind of knew I was going to lose the yellow jersey here, but it was a special occasion for me coming back here. It was a great day," said the Dutch rider who climbed top of the overall rankings Thursday.
The day's action revolved around two ascents of the Mur de Bretagne, a 2km climb at an average of six per cent, that has been written into Tour de France folklore.
With the Tour returning to Brittany after a four-year gap, huge festive crowds packed the villages and pretty country lanes as the temperature hit 30 degrees Celsius (86 Fahrenheit).
The 179 remaining riders left Saint Malo on the north-west coast, passing the magnificent Sillon beach with its granite sea wall and chic seafront buildings.
Injured Almeida rides on
Key Pogacar teammate Joao Almeida fell ahead of the second climb of the Mur de Bretagne, but despite sustaining a rib fracture, he is due to make the start line for Saturday's flat run to Laval.
"I really hope he's okay, he's on his way for an X-ray. I'm proud of how he's been riding. He's done an amazing job. It would have been a perfect day," Pogacar said.
"I dedicate this victory to him," he added.
Later, UAE's team doctor Adrian Rotunno reported: "It's confirmed he has an uncomplicated left-sided rib fracture, as well as some profound abrasions to his body. Fortunately, no concussion."
Rotunno added: "The next few days will be difficult for him, but at this point, he should be able to start tomorrow's stage."
In the best form of his career, Almeida had been a candidate for a place on the podium in Paris, but has slipped to 12 minutes 21 seconds off the pace in the overall standings.
For Bahrain Victorious, their Tour de France appears massively compromised.
Not only did the Australian rider Jack Haig leave the Tour after the fall 6km from the line, but their leader Santiago Buitrago finished 13 minutes down on the day and left the medical centre holding his right arm to his side.
One man who negotiated the crash well was Ireland's Ben Healy.
The sixth stage winner managed to fall sideways into the heap and roll over it, before remounting immediately to finish a respectable 26th.