The 24-year-old was selected ahead of Chris Hoy, the 2008 Olympic champion in the event, as the number of riders in individual events is limited to one rider per nation.
Kenny, who won silver in China aged 20, clocked 9.713 in the ranking round, improving the mark of 9.815 Hoy set en route to gold four years ago.
World champion Gregory Bauge of France was second quickest in 9.952, with Australia's Shane Perkins third in 9.987 and Germany's Robert Forstemann fourth in 10.072.
The result saw Kenny claim top seeding and, with 17 riders entered, he skipped a phase of the gruelling three-day competition.
There was misfortune for Spain's Hodei Mazquiaran Uria, who required a second ride after his saddle disintegrated on the flying lap of his third attempt.
He finished in 10.604 and was set to face Perkins in the first round, with Bauge poised to ride against Zafeirios Volikakis of Greece.
In the first of six disciplines in the omnium, Ed Clancy, fresh from claiming Team Pursuit gold with Great Britain on day two, finished first.
Clancy clocked 12.556 in the flying lap, more than half a second clear of the field.
Shane Archbold of New Zealand was second in 13.112, with world champion Glenn O'Shea of Australia third in 13.222.