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The eight-times world champion ended the second leg of the season-opening event with a lead of 1min37s over Spaniard Dani Sordo (Mini) with Ford's Norwegian Petter Solberg third and another three seconds back
Loeb's former team mate Ogier, driving a Super 2000 specification Skoda before returning to VW for a full challenge in 2013, had kept up with the leaders in icy conditions but crashed on the day's final stage.
He and co-driver Julien Ingrassia were unhurt.
TOUGHEST RALLY
HELPING HANDS: Spectators help French driver Renaud Poutot get back on the road.
Loeb, fastest on five of the day's six stages, said: "Today was easier than Wednesday, more like a normal tarmac rally, but it was still tricky because it was very muddy in places butut I was feeling good so I tried to push. I don't know what will happen on Friday and with the conditions suiting me today I tried to take everything I could.
Citroen's Mikko Hirvonen, 2010's overall runner-up who has moved from Ford to become Loeb's team mate, was fourth.
The Monte, the most prestigious and historic rally in the championship, as well as one of the toughest, will end in the Mediterranean principality on Sunday after 18 special stages, including the spectacular Col du Turini.