Millar raced from Saint-Jean-de-Maurienne to Annonay Daveziex in 5 hours, 42 minutes and 46 seconds.
France's Jean-Christophe Peraud was second in the 226-kilometer (140-mile) run -- longest of the tour this year.
Overall race leader Wiggins has a 2:05 advantage over countryman Christopher Froome and is 2:23 ahead of Italy's Vincenzo Nibali.
The Stage 13 run Saturday covers 217 kilometers (134 miles) over a route that is mostly flat.
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