Pogacar, who rides for UAE Team Emirates, finished the short but extremely challenging 94.4-kilometer (58.6-mile) stage in 2 hours, 58 minutes. Quintana crossed the line next as the rider for Movistar took the red leader's jersey from Nicolas Edet, who was dropped early in the stage.
The highly anticipated stage in the Pyrenees shattered the peloton with five summit climbs and a 4-kilometer (2 1/2-mile) gravel track near the end, which the riders reached amid heavy rain and hail. The strongest of the favorites for the Grand Tour all finished within a minute of each other, leaving them in a tight bunch ahead of the first rest day.
Primoz Roglic overcame signs of weakness and finished in third, as the Slovenian moved to second overall at six seconds behind Quintana. Fellow contender Miguel Ángel López looked like he was going to deal a blow to his rivals after he dropped them with a powerful attack. But he fell on the gravel stretch when the weather was at its worst. The Colombian finished the stage ninth and is third overall at 17 seconds behind fellow countryman Quintana.
López said the stage should have been stopped because of the weather. A mountain stage was halted in the Tour de France in July when rain made the course impossible to ride. "I have my arms scraped up," López said. "It was very dangerous. At least there wasn't a descent."
World champion Alejandro Valverde, a teammate of Quintana, is fourth at 20 seconds back. The racing resumes Tuesday with an individual time trial across the border in France. Roglic is considered the best suited of the top riders to make big gains on the 36 kilometers (22.3 miles) from Jurancon to Pau.
"The important thing was to try to take some time on Roglic, who should do well on the time trial," said former Vuelta winner Quintana.
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