The Team Sky rider, 23, surprised the field on the 24-kilometre time-trial around Big Bear Lake with a four-second victory over American Brent Bookwalter.
Dibben, in his first year with Team Sky, won in 28 minutes and 27 seconds.
"When I crossed the line I didn't know I'd set the fastest time for a couple of minutes," he told Team Sky.
"I guess I'd have been happy with a top 20 so to win is pretty good."
New Zealand's George Bennett goes into Saturday's seventh and final stage with a 35-second overall lead on Poland's Rafal Majka.
Britain's Jonathan Dibben secured his first victory on the World Tour circuit by winning stage six of the Tour of California.