The Dakar is being held entirely in Saudi Arabia this year after the last decade in South America.
Peterhansel has now won a Dakar stage on all three continents that have hosted the rally, from its origins in Africa.
Peterhansel had been due to compete with his wife Andrea, who finished fifth in 2004 under her maiden name of Mayer, as co-driver but she was ruled out on health grounds last month, with Portuguese Paulo Fiuza stepping in.
Two-time Formula One champion Fernando Alonso, who lost two and a half hours on Tuesday with a broken wheel and suspension, fell further behind the leaders in his Toyota Hilux pickup.
SA's Giniel de Villiers finished Wednesday's stage sixth in his Toyota Hilux. He now lies seventh overall.
In the motorcycle category, American Ricky Brabec retained the overall lead, two and a half minutes ahead of Argentine Kevin Benavides.
Britain's Sam Sunderland was fastest on the stage, but then collected a five-minute penalty for speeding, dropping the KTM rider to eighth, with Chile's Jose Ignacio Cornejo taking a first stage win instead for Honda.