Stephane Peterhansel took the lead in his Mini Countryman after the opening stage winner Carlos Sainz had navigation issues during the 242 km long second stage. (Getty Images)
South Africa's Giniel De Villiers, another experienced Dakar campaigner in his Toyota, was second on the day, 2 minutes 35 seconds behind while French driver Ronan Chabot, in an SMG, was third, 3 minutes 52seconds off Peterhansel's pace.
"We had a good stage, mainly thanks to navigation. We're fast, and we've got the potential to go even faster, but it was mostly (co-driver) Jean-Paul Cottret's navigation which saved the day, nothing else," said Peterhansel.
Overnight leader Sainz, the 2010 champion, endured a nightmare session, getting lost at the 75 kilometres mark, and finished outside of the top 10.
Buggy teammate al-Attiyah, the 2011 winner, was sixth on the stage, 11 minutes 37 seconds behind and is also sixth overall, more than 10 minutes behind Peterhansel.
Spain's Joan Barreda Bort, riding a Husqvarna, won the motorcycling stage and also took over the overall lead.
Barreda Bort won in a time of 2 hours 42 minutes 31 seconds with compatriot Juan Pedrero Garcia, on a KTM, in second place, 3 minutes 12 seconds behind.
Australia's Matt Fish, on another Husqvarna, was third, 5 minutes 53 seconds behind the leader.