Pogačar also took a 10 second time bonus for the win.
He leads his nearest rival, last year's runner-up Geraint Thomas of Wales, by 45 seconds.
It made up for the disappointment of being pipped to the line in a sprint yesterday, eventually finishing third behind Jhonatan Narvaez of Ecuador and Max Schachmann of Germany.
It's the Slovenian's first time riding the race and many are tipping him for overall victory, after an excellent start to the season.
He has already had victories in the Volta a Catalunya stage race and the 1-day classics Strade Bianche and Liege-Bastogne-Liege.
Pogačar also leads the mountains classification at this early stage of the season's first Grand Tour.
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