The Pole, who also won the race in 2014, attacked a group of leading riders with about 12 kilometres left and never looked back.
Kwiatkowski, who had not won a race since claiming the GP E3-Harelbeke almost a year ago, always looked comfortable on the white gravel sections of the 175km ride.
World champion Peter Sagan abandoned after starting the race feeling unwell.
Olympic champion Greg van Avermaet of Belgium took second place ahead of his compatriot Tim Wellens.
The UK Anti-Doping chief executive officer told a British parliamentary select committee this week that there were "zero records" from a doctor who delivered a package to Team Sky rider Bradley Wiggins at a race in France in 2011.
Committee chairman Damian Collins said after the hearing that the "credibility of Team Sky and British Cycling is in tatters".
(Reporting by Julien Pretot; Editing by Ed Osmond)
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