Claudio Chiappucci of Italy, who has finished in the top six of the Tour since 1990, dropped out before the start of the 12th stage, plagued by a virus.
The stage of 204 kilometers (127 miles) had two major climbs, the famous Tourmalet, 2,115 meters and Luz Ardiden, 1,715 meters.
Virenque pulled far ahead of the pack, and only Marco Pantani of Italy stayed within five minutes of him starting the final climb to Luz Ardiden. Pantani ended up 4 minutes, 34 seconds behind.
Indurain and his Banesto teammates allowed Virenque and Pantani to gain the advantage because they trailed Indurain by more than 15 minutes each entering the day's leg.
Indurain came in more than seven minutes back but ahead of the main pack. His main rival, Tony Rominger of Switzerland, lost more than three minutes to Indurain and is now 7:56 behind the three-time defending champion.
Chiappucci was more than 33 minutes behind in the overall standings when he decided to stop. He barely moved from his hotel room during the off day in Lourdes on Thursday, suffering from what his team manager said was an intestinal virus.
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