Conti took control of a small group that broke away from the main pack at the bottom of the final 1,860-meter ascent. He went out on his own with about 10 kilometers left and won by more than two minutes over Hernan Buenahora of Colombia.
Starting Tuesday's stage, Conti was almost 18 minutes behind Indurain in the overall standings and gained about 10 minutes with his performance.
After Virenque, second overall, took off alone on the final mountain, gaining a 90-second edge, Indurain responded. With less than three kilometers left, Indurain increased the pace, and ended out finishing only 35 seconds behind Virenque, who now trails in the overall standings by 7:21.
There are three more days left in the Alps, however none of Indurain's top rivals are left.
Tony Rominger, Claudio Chiappucci and Gianni Bugno, who placed second to Indurain the last three years, are all out due to virus or exhaustion.
Three-time champion Greg LeMond -- the last person before Indurain to win the Tour de France -- dropped out a week ago. Lance Armstrong, who succeeded Bugno as world champion, dropped out Monday.
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