With two-time Olympic keirin champion Sir Chris Hoy on a break from international competition, Kenny, who won gold in both team and individual sprint in London, found himself having to step into the shoes of his team-mate.
After a storming ride in the semi-final Kenny looked on course to take the gold at the Sir Chris Hoy Velodrome, but an over ambitious move on the final lap led to a touch of wheels which saw the rider come crashing to the ground, taking French rider Quentin Lafargue with him.
Stefan Boetticher (Germany) won gold, with Australian Peter Lewis (Team Jayco-Ais) clinching silver and Takashi Sakamoto (Japan) the bronze.
While Jess Varnish and Becky James combined their fire power to take team sprint gold on Friday, they found themselves going head-to-head in the semi-final of yesterday's individual event. After three fiercely-contested rounds of calculated cat-and-mouse tactics mixed with explosive strength, Varnish emerged triumphant. She progressed to the final against Kristina Vogel (Germany), but her battle against James had clearly taken much out of her and she had to settle for silver. James overcame Wai Sze Lee (Hong Kong) to win bronze.
Their medal haul will go some way to helping put the disappointment of London behind them where James, 20, failed to make the final Olympic squad and Varnish, 21, lost her chance of a medal when she was disqualified in the opening round of the team sprint alongside Victoria Pendleton.
"I'm pretty happy with silver," said Varnish. "I need to step it up a level now and win finals. It's the first individual final I've made in a world cup."
After taking gold in the team pursuit on Friday, double Olympic champion Laura Trott began her campaign in the omnium.She expressed some trepidation beforehand, but resolved to focus on the task at hand. "I'm not really looking forward to it; it's going to be hard," she said. "I just love riding my bike and that's it, really. That will get me through, hopefully."
Trott, reigning Olympic and world champion in the event, finished fourth in the flying lap and ninth in the 20km points race. At the end of two rounds, she lay in sixth position with the individual pursuit, scratch race and time trial, her strongest events, still to come.
There was disappointment in the men's individual pursuit, with Britain's Andy Tennant clearly still feeling the after effects of Friday's dramatic crash in the team pursuit which left him with six stitches to his right knee. Despite a pacy start in qualifying, Tennant faded in the final laps to finish fifth.
British Cycling Olympic Academy rider Lewis Oliva, competing for Wales, was another who come into contact with the unyielding Siberian pine boards. He had to be stretchered from the track after a nasty collision with Denis Dmitriev (Team RVL) in the keirin semi-final. He escaped broken bones but a decision will be made this morning on whether he is fit to contest the men's individual sprint today.
The conclusion of the men's omnium, meanwhile, saw Lucas Liss (Germany) take gold, Glenn O'Shea (Australia) silver and Unai Elorriaga (Spain) the bronze. Britain's Jon Dibben finished in fifth.