Kwiatkowski recorded the quickest time on the short 5.57-kilometre course, of six minutes 22 seconds, to beat Rohan Dennis of Australia by two seconds and Germany's Marcel Kittel by four seconds.
Triple world time-trial champion Tony Martin of Germany settled for fifth place, five seconds off the pace, while Italian Giacomo Nizzolo squeezed home in fourth spot.
Defending Romandie champion and Tour de France holder Chris Froome of Sky came home 13th, ten seconds behind Kwiatkowski's winning time, while overall contender and Giro d'Italia champion Vincenzo Nibali was two seconds slower in 18th.
"It's a big surprise," said Kwiatkowski, who takes the leader's yellow jersey.
"I was in form for the Ardennes classics but I didn't know what kind of form I would be in today," he said.
"I'm really happy with what I've done," Kwiatkowski said.
"To have a few seconds advantage is something special."
The first stage proper is scheduled for Wednesday and a 200.9-kilometre run from Ascona to Sion which will feature the snow covered Simplon climb.
The six-day race finishes on Sunday with a 18.5km time-trial around Neuchâtel.