Pereiro leads American Floyd Landis by 1 minute, 29 seconds.
Fedrigo passed Salvatore Commesso of Italy during the last few moments of Sunday's 181-kilometer stage and out-sprinted Commesso to the finish.
American Christian Vandevelde finished in third, three seconds behind the leaders, followed by France's Christophe Moreau and Austrian Georg Totschnig.
With 40 kilometers to go, Matthias Kessler of Germany, Belgian Rik Verbrugghe and David Canada of Spain crashed on a corner, forcing the latter two riders to withdraw from the race. Canada broke his collarbone and Verbrugghe fractured his thigh.
Stage 15 is 187 kilometers long. The 2006 Tour will end July 23 on the Champs-Elysees in Paris.
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