Spain's Alejandro Valverde won the tour's first Alpine 110.9-mile stage by a hair in 4 hours, 50 minutes, 35 seconds. However, Armstrong's Discovery Channel team leads the overall standings by 38 seconds over Denmark's Michael Rasmussen.
The stage was shortened from 119-miles to 110.9-miles and delayed for nearly 40 minutes because of a farmers protest.
Germany's Jens Voigt, who started the day in yellow, dropped out of the top 10 standings.
Ivan Basso, who was also left far behind in the ascent is third, 2:40 behind.
Earlier Tuesday, Russia's Evgeni Petrov was thrown out of the race after failing a blood test, the BBC said. The 27-year-old had been in 45th overall in the race.