In the colours of Poland, Kwiatkowski put in a strong ride across the 52.5-kilometre course in Austria, finishing 43 seconds off a bronze medal.
The day was dominated by Rohan Dennis (Australia), with the BMC Racing rider going fastest through every split to set an unbeatable time of one hour, three minutes and two seconds.
Tom Dumoulin (Holland) came home 1:21 back, with Victor Campenaerts (Belgium) rounding out the podium just half a second behind.
Kwiatkowski was joined by Jonathan Castroviejo and Vasil Kiryienka in the top 10. Castroviejo took sixth place for Spain while Kiryienka, world champion himself in 2015, picked up ninth.
Pavel Sivakov (Russia/33rd) and Tao Geoghegan Hart (Great Britain/35th) gained great experience at the elite level, with all five riders set to feature in Sunday's road race.