Kwiatkowski, who will be one of four-times champion Chris Froome's lieutenants on the Tour next month, clocked seven minutes 25 seconds in Valence.
He beat Dutchman Jos van Emden and Italian Gianni Moscon, who were second and third, by one and three seconds respectively.
Briton Geraint Thomas, who seemed en route for the stage win, crashed and ended up 21 seconds off the pace.
Overall contender Romain Bardet of France lost 23 seconds, with 2014 Tour champion Vincenzo Nibali of Italy ending up 24 seconds behind Kwiatkowski.
Froome, who won the Giro d'Italia last month, is not taking part in the race.
(Reporting by Julien Pretot; Editing by Clare Fallon)
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