The 22-year-old, who rides for the VolkerWessels cycling team, beat countrywoman Scarlett Souren by 14 seconds overall in the three-stage 243.7 km race.
Polish cyclist Katarzyna Wilkos placed third in the final standings, 27 seconds behind Molenaar.
The second-fastest Pole, Olga Wankiewicz, finished fifth overall, 39 seconds behind the winner.
The Netherlands' Souren was named the most active rider in the race, which was held for the second time after an eight-year hiatus, attracting nearly 80 cyclists from 16 teams based in various countries.
The race ran through cities such as Lublin, Krasnystaw and Kraśnik.
Souren won the last, 103.1 km, leg of the race from the picturesque spa town of Nałęczów to the historic town of Kazimierz Dolny in Poland's eastern Lubelskie region on Sunday.
Race director Czesław Lang said that the 2nd Tour de Pologne Women was "a beautiful three-stage race full of emotion and dynamics, leading through amazing places."
He added: "Each stage was a thrilling experience with a high level of sportsmanship. We have achieved what we wanted, to develop women's cycling in Poland. We have great riders, such as Kasia Niewiadoma, but we don't have world-class events. We want to bring Tour de Pologne Women to the same class as the men's race."
The men's Tour de Pologne, Poland’s largest cycling race, will be held for the 81st time from August 12 to 18.
(gs)
Source: TVP, PAP, tourdepolognewomen.pl