Poland's Majka had taken the lead after his win on stage two, but will now find himself chasing Team Lotto's Bennett on the final day to Pasadena.
Dibben clocked 28 minutes, 27 seconds on Friday, with Brent Bookwalter of BMC seven seconds further back.
Andrew Talansky, who won Thursday's fifth stage by two seconds, finished the time trial in third, nine seconds behind Bookwalter, who is fourth overall.
Ian Boswell of Team Sky is fifth and a minute behind Bennett, who expressed surprise to finish the day with the yellow jersey.
"I'm the most surprised guy that watched the time trial or who was part of the event today," Bennett told reporters. "I never thought I would be here.
"When I looked at the profile of the time trial course it was fast and furious. You just needed a lot of power today and that's not what I have.
"I don't now where it came from."
Britain's Dibben added he was equally surprised at his stage victory.
"I think George said it was disbelief, and I can certainly tell you it's certainly a bigger shock for me," Dibben said.
"I just sort of went out there and let the pain come to me. After a few K I was already screaming and I just kept digging in."
(Writing by Jahmal Corner in Los Angeles; Editing by Greg Stutchbury)
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