Contador, Armstrong's Astana teammate and the 2007 Tour champion, increased his overall lead in the 18th stage in which cyclists rode against the clock on the 25-mile course in and around Annecy.
The three-week race ends Sunday on the Champs-Elysees in Paris.
Contador finished in 48 minutes, 31 seconds, beating Fabian Cancellara, of Switzerland, by three seconds. Russia's Mikhail Ignatiev was third, 15 seconds back.
"I went all out," said Contador, adding his earpiece radio linking him to team managers stopped working during the stage and he was worried about Cancellara's skill at time trials.
"Of course, what I especially wanted was to think about general class. A stage victory was less important," he said. "I'm very happy. I didn't expect it."
Armstrong was 16th, 1:30 behind. But he easily overcame a 30-second deficit to Frank Schleck, who began the day in third place but slipped to sixth after finishing 2:34 behind Contador. Armstrong had "mixed emotions" about his ride.
"Sixteenth in a time trial is not a good result," he said. "But my ambition is to get on the podium, so I have to be happy with that."
Schleck and younger brother Andy had bumped Armstrong from second place to fourth a day earlier in the last punishing Alpine stage.
"I suffered," Armstrong said. "I probably started too hard and maybe I was just empty from yesterday and those cramps I suffered at the end of the (17th) stage."
Overall, Contador leads Andy Schleck by 4:11. Armstrong is 5:25 back.
While the stage was mostly flat, riders had to contend with the Bluffy pass climb, which snaked upward for more than 2 miles with magnificent vistas over the hill-ringed lake.
Armstrong was relatively strong at the start, only 29 seconds slower than Contador through the second intermediate time check at the 25-kilometer mark. His main time deficit came on Bluffy, where he was 1:12 behind Contador.
A 25-mile individual time trial around Annecy Lake.
WINNER: Alberto Contador, of Spain, three seconds ahead of time-trial specialist Fabian Cancellara, of Switzerland. Mikhail Ignatiev, of Russia, finished third, 15 seconds off the pace, while seven-time champion Lance Armstrong was 90 seconds behind in 16th.
YELLOW JERSEY: Contador, the 2007 winner, leads Andy Schleck by 4:11. Armstrong climbed to third, 5:25 behind his Astana teammate.
QUOTE OF THE DAY: "We must absolutely make no mistakes on the climb of Mont Ventoux." -- Contador, about Saturday's penultimate stage, featuring a 13-mile ascent at an average gradient of 7.6 percent .
NEXT STAGE: Today's stage is a 111-mile ride from Bourgoin-Jallieu to Aubenas. The course features three little climbs and is likely to favor breakaway riders.
LANCE'S NEW RIDE
Lance Armstrong and RadioShack are forming a new cycling team that will compete in next year's Tour de France.
The seven-time Tour winner, who returned to cycling after 31/2 years of retirement, also said Thursday he expects to take part in running and triathlon events for Team RadioShack beginning in 2010.
The 37-year-old Texan is riding this year's Tour with the Kazakh-funded Astana team. He was in third place overall after Thursday's time trial, 5 minutes and 25 seconds behind teammate Alberto Contador.
In a statement released by RadioShack, Armstrong said he has had "a great season so far" but is hoping for an even better one next year.
"To be able to compete for an American team comprised of the world's top cyclists, supported by the best coaches and staff -- I couldn't be happier," he said.