Frenchman Christophe Laporte (Jumbo) retained the leader's yellow jersey despite an apparent minor fall in the last few hundred meters.
In an uphill sprint, Pedersen beat Frenchman Bryan Coquard and Belgian champion Wout van Aert.
Aged 26, the Dane, world champion in 2019, took his 20th victory, the second of the season.
The winner of the day before, Dutchman Fabio Jakobsen, was left behind by the peloton led by van Aert's teammates on the last climb of the course, before the last 20 kilometers.
A breakaway of three riders (T. De Gendt, Doull, Gougeard), in the lead from the first minutes, was caught 24 kilometers from the finish.
Wednesday, the only time trial of the event is run over 13.4 kilometers in the Allier, from Domérat to Montluçon, and ends with a steep climb (700 m at 8.6%).
© 2022 AFP