Six-times Olympic champion Kenny was making his international return after taking a break from the sport following the 2016 Rio Games but could not mark it with another gold.
The flying Dutch trio of Nils van ’t Hoenderdaal, Harrie Lavreysen and Jeffrey Hoogland won the final by half a second from Britain with France beating Russia for the bronze medal.
Earlier in Apeldoorn velodrome, 35-year-old Kirsten Wild won the women’s 10km scratch race ahead of Belgium’s Jolien D‘Hoore to take her haul of world championship medals to seven.
Denmark’s Amelie Dideriksen was third.
Wild chased down an early attack by Ireland’s Lydia Gurley and went solo to the line.
”It’s really, really nice to win, for my own people, it’s amazing,“ Wild said. ”It’s the best riders of the world to compete and I can’t believe that I won solo.
“My tactic was to stay really calm in the peloton and wait for the sprint, but it didn’t go quite to my plan.”
The Dutch could not quite make it a clean sweep of the golds on day one as they had to settle for silver in the women’s team sprint won by the Kristina Vogel-powered German team.
“We did a very good job, and it is just incredible to win the gold medal and be world champions,” said Vogel who won the individual sprint gold in Rio.
“It has been four years since we won the gold medal (in the team sprint) so it is very special.”