Mini driver Peterhansel, who is bidding for a 10th win in the Dakar after having already won six times in the motorbikes and three times in the cars, clocked 3hr 56min 53sec over the 598km stage, which featured a 478km timed run.
Spanish driver Nani Roma came in second in his Mini at 3:44, with Portugal's Ricardo Leal Dos Santos, also in a Mini, 8:56 behind Peterhansel's pace.
"There wasn't much visibility, even opening the road, because the wind blew the dust up making it difficult to see," said Peterhansel, who stretched his lead in the overall standings from Roma to 22:49.
"There's around twenty minutes between Nani and me now, with two big stages of dunes to come. We'll have to play it safe. It's always been like that. Each time I've won the car race, I always had a team-mate hot on my heels: Masuoka, Alphand. There's always been this sort of pressure to handle."
There was drama in the motorbike section as France's Cyril Despres claimed his fourth stage win to extend his overall lead on Spain's defending champion Marc Coma.
Despres - whose relations with KTM team-mate Coma deteriorated after stewards halved the Frenchman's huge deficit on Monday's stage - added more than two minutes to his advantage on the Spaniard to 2min 22sec in the overall standings.
"It was a tough day, all in all! An important development might be if someone moves in between Marc and me. Tomorrow will be complicated, but anything can happen on the Dakar," said Despres.
It was also the French rider's 30th stage victory on the Dakar.
He finished the 534km special (705km overall) 1min 39sec ahead of another KTM rider Gerard Farres Guell of Spain with Coma third at 2min 01.
Coma warned: "I'm going to try my utmost right until the end. There are three days left to give it everything."
Friday sees competitors race the 12th 657km stage between Arequipa and the central-southern town of Nasca, including a 245km special.
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