“I switched my focus around 2k to go to prepare for sprint and it worked,” said Pogacar.
“I knew that Van der Poel was the fastest, obviously, in this group. But after a finish like this, you cannot count all of the rest out.”
Pogacar earned 10 bonus second for his win, while Vingegaard received six seconds and Van der Poel four.
The Criterium du Dauphine will be contested over eight stages, which include a time trial, as the riders prepare for the start of the Tour de France on 5 July.
Stage two on Monday will be a 204.6km run from Premilhat to Issoire.