Belgium's Kopecky (SD Worx-Protime) was in a lead group of six when the 148.5km race arrived at the famous Roubaix Velodrome and had enough in the tank to outpace her rivals.
Elisa Balsamo (Lidl-Trek) finished second while Pfeiffer Georgi (DSM-Firmenich PostNL) pipped Marianne Vos (Team Visma-Lease a Bike) to third place.
Vos made the first move on the velodrome lap and led into the final straight but Balsamo went past her before Kopecky timed her victory surge to perfection.
"This was the goal of the season, to also do it is really nice. The team gave me so much confidence the whole season already, but especially the last week," Kopecky said.
"It's always nervous, you are here with two very fast sprinters, Vos and Balsamo, so you're never sure."
The men's race takes place on Sunday when Mathieu van der Poel will be aiming to retain his title and make it a golden double after winning last week's Tour of Flanders.
