Jakobsen underwent five hours of surgery overnight after an 80km/h finish-line crash on Wednesday’s opening stage blamed on his Dutch compatriot Dylan Groenewegen.
Pedersen started the day in his world road-race champion rainbow jersey, but ended it in the Tour of Poland overall leader’s yellow after the run from Opole to Zabrze.
“I dedicate this win to Jakobsen and wish him a speedy recovery, hope he gets back to a normal life and back to cycling,” said Pedersen.
His bunch sprint win on Thursday came as a surprise for a man more adept at long range wins, but was planned, according to the 24-year-old Dane.
“Yeah, we planned it like that, that the lead out train would work for me, and it did work,” Pedersen told Polish television.
Groenewegen apologised on Thursday after severe cristicism for his role in the crash with rival team manager Partick Lefevre filing a police complaint against him and calling for him to be thrown in jail.
Doctors said Jakobsen, of the Deceuninck-Quick Step team, was in a “serious but stable condition” after five hours of surgery to the head.
The Tour of Poland goes into the mountains on Friday with a 203km run from from Wadowice to Bielsko-Biala in the south of the country.
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