Vinokourov, who finished third overall behind Armstrong and Jan Ullrich of Germany in 2003, pipped fellow escapee Santiago Botero of Colombia to win the stage after a 172km ride from Courchevel to Briancon.
Armstrong came in 1minute 15seconds behind in a group of riders and did not contest the sprint that saw France's Christophe Moreau take third place on the day.
However, the Texan is still the proud wearer of the leader's yellow jersey with a lead of 38 seconds over Michael Rasmussen of Denmark.
The day also saw the Tour further tarnished by another drugs scandal, with Italian rider Dario Frigo quizzed by police after banned substances were found in a car driven by his wife.
Vinokourov also picked up 36 bonus seconds but is only 12th overall and some 4min 47sec behind Armstrong who looks to be as strong as ever in his final ride in the Tour he has dominated since his near-miraculous recovery from life-threatening cancer in the late 1990s.
The American is still well on course for a seventh consecutive win in the race no other rider has won more than five his last of an outstanding career before retirement.
Vinokourov had been one of many riders who had been blown away by a superb Armstrong in Tuesday's 10th stage but at least the Kazakh rider could celebrate his third career stage win in Le Tour.
Vinokourov does not believe his bad day on Tuesday has eliminated him from the race for overall honours with Armstrong's grip on the yellow jersey looking tighter than ever.
"The Tour is not over," said the Kazakh champion. "There are still 11 days to go and with this team my morale is a lot higher."
In truth, with a six minutes 38 seconds lead at the start of the day over Vinokourov, Armstrong was never concerned about chasing the Kazakh, and only Botero made a serious attempt to contest the stage.
The American instead, surrounded by his usual praetorian guard of riders from the Discovery Channel, remained in charge of the peloton and although at one point Vinokourov had three minutes on the Texan the gap dwindled on the descent of the Col du Galibier, one of the most famous climbs in the Tour.
Vinokourov's display and Armstrong's dominance were nonetheless overshadowed by the controversy surrounding Frigo, who was detained, and could not start the race.
The incident follows the expulsion of Russian rider Yevgeny Petrov, who was thrown out after failing a drugs test.
The peloton has a relatively easy 187km from Briancon to Digne-les-Bains today.