Luc Leblanc of France captured the 11th stage as the race entered the mountains after 10 days of flat cycling. But Indurain was the real victor, increasing his margin over second-place Tony Rominger by more than two minutes.
Rominger, who weakened up the final hill, now trails the Spaniard by nearly five minutes in the overall standings.
A five-man group that included Stephen Swart of New Zealand went out ahead after 134 kilometers and established a five-minute lead.
However they were reeled in at the base of Mount Hautacam with 13 kilometers to go.
Leblanc and Indurain stayed together until the final straightaway with Leblanc moving away to the stage victory. Indurain was content with second. Pantini was third.
Earlier in the day, Chris Boardman, who became the first Briton to take the race leader's yellow jersey in 32 years, dropped out of the race.
"I did not want to destroy everything by forcing myself on just to ride in the Pyrenees, as much as I would have liked to have done," said Boardman, who retired after 100 kilometers of Wednesday's stage.(AP, Reuters)
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