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Vingegaard made his move with 4.3 kilometres remaining in the first summit finish of the Race to the Sun, but was kept close by his Tour de France rival in what was their first encounter of the season.
The Jumbo-Visma star's attack prompted Pogačar to launch one of his own soon after and while Vingegaard was initially able to hold on, a subsequent burst through a bend ultimately proved his downfall.
Pogačar's advantage over Vingegaard then increased as he made contact with David Gaudu (Groupama-FDJ) in the final two kilometres, where the pair marked each other closely before the UAE Team Emirates rider kicked clear within 100 metres of the line.
Gino Mader (Bahrain Victorious) was next to cross in third and was followed by Aurelien Paret-Peintre (AG2R Citroen) and Kevin Vauquelin (Arkea-Samsic) until Vingegaard carried himself over in sixth.
It was a surprising sight, according to Pogačar, who expected more from the man who put an end to his two-year reign at the French Grand Tour in 2022.
"I was a little bit [surprised]," Pogačar said. "First he launched the attack and thought he was feeling super, super great, so I didn't counter - I was waiting for the rest.
"In the end, it was really tough and I think he just missed a little bit to catch me then he couldn't close and cracked a little bit."
Pogačar holds a 44-second lead over Vingegaard as a result, with his effort in the 165km stage enough to propel him into the overall lead with four stages remaining.
Stage 5 is the longest of this year's Paris-Nice at 221.4 kilometres and will contain five modest climbs despite its predominantly flat terrain. SBS and SBS On Demand will broadcast the stage live and free from 12:55am (AEDT) on Friday, March 10.
