The 51-year-old, looking to win the race for the fourth time, finished the stage 12 minutes and seven seconds quicker than nine-time world rally champion Sebastien Loeb in second place.
The 333-kilometre loop around northern Saudi Arabia saw several competitors suffer navigational difficulties, resulting in large time gaps.
Record 14-time Dakar winner Stephane Peterhansel, nicknamed "Monsieur Dakar", lost a lot of time after a puncture to his Audi.
Australian Daniel Sanders extended his early lead in the bikes category, beating Chilean Pablo Quintanilla by 3mins and 7secs on Sunday.
