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American Van Garderen was the last to ride the hilly and technical course, completing the 31.2-kilometre (19.6-mile) route in 48 minutes, 52 seconds.
"I don't want to count my chickens before they hatch, but I'm ready to win, and it's about time," said van Garderen, who finished fifth in the event in 2011 and fourth last year. "Now I'm finally mature enough to pull through to the end. I'm ready to do it."
Dutchman Lieuwe Westra of Vacansoleil-DCM, the stage one winner, was second in 49:15 while Australia's Rohan Dennis of RadioShack Leopard was third in 49:20.
Rogers, the Saxo-Tinkoff rider and three-time world time trial champion, was fourth but 1:05 behind van Garderen, putting him 1:47 seconds overall behind the BMC rider with two stages left in the eight-day race.
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Rogers and several other top contenders opted to switch from time trial to road bikes to negotiate the steep final climb.
"It was a steep climb, for me maybe too steep for the time trial bike, the gearing was more suitable on the road bike," said Rogers, the 2010 Tour of California winner. "It was a perfect climb because it was steep straight away, and the speed dropped very fast. I took advantage of the speed being low and changed," he said.
Van Garderen remained on his time trial bike the entire route.
"There was really no place that you could hold back," said van Garderen, who was fifth last year as the highest-finishing American in the Tour de France. "I started straightaway up that climb. You just had to dig deep there. The climb up to the finish was hard. There was a couple of little downhills that you could kind of soft-pedal and catch your breath a little bit."
Australia's Cameron Meyer of Orica GreenEdge jumped from sixth to third overall with a sixth-place finish in the stage. He trails van Garderen by 2:57.
American Dave Zabriskie, the four-time Tour of California race runner-up, crashed out of the event while training on the time trial course.
The eight-day event continues Saturday with the 146.3-kilometre (91.4-mile) stage from Livermore to Danville. The route will finish with an 18.4-kiometre (11.5-mile) ascent to Mount Diablo
The race concludes Sunday with a 128.1-kiometre (80.7-mile) morning road race from San Francisco to Santa Rosa.
STAGE SIX RESULTS
1. Tejay van Garderen (BMC), United States, 48 minutes, 52.37 seconds.
2. Lieuwe Westra (Vacansoleil-DCM), Netherlands, 49:15.24
3. Rohan Dennis (Garmin-Sharp), Australia, 49:20.70
4. Michael Rogers (Saxo-Tinkoff), Australia, 49:57.77
5. Marco Pinotti (BMC), Italy, 50:00.57.
6. Cameron Meyer (Orica-GreenEdge), Australia, 50:20.25
7. Bob Jungels (RadioShack), Luxembourg, 50:21.26.
8. Leopold Konig (NetApp-Endura), Czech Republic, 50:35.97
9. Frank Mathias (BMC) Switzerland, 50:38.29
10. Sylvain Chavanel (Omega-Pharma Quickstep), 50:40:52
Overall Classification
1. Tejay van Garderen (BMC), United States
2. Michael Rogers (Saxo-Tinkoff), Australia, 1 minute, 47 seconds behind.
3. Cameron Meyer (Orica-GreenEdge), Australia, 2:57 behind.
4. Mathias Frank (BMC), Switzerland, 3:21 behind.
5. Janier Acevedo (Jamis-Hagen Berman), Colombia, 3:31 behind.
6. Matthew Busche (RadioShack), United States, 3:33 behind.
7. Francisco Mancebo (5-Hour Energy/Kenda), 4:26 behind.
8. Philip Deignan (UnitedHealthcare), Ireland, 4:52 behind.
9. Chad Haga (Optum/Kelly Benefit) United States, 5:02 behind.
10 Lawson Craddock (Bontrager), United States, 5:04 behind.
