De Villiers was fifth in the stage, the longest of the race, but with Qatar's Nasser Al-Attiyah dropping out of contention, he jumped one spot in the standings and opened a gap of more than six minutes over third-placed Russian Leonid Novitskiy.
The South African, however, remained 49 minutes behind runaway leader Stephane Peterhansel of France.
Sarel van Biljon, the only South African rider in the quad bikes division, saw his race come to a halt after he withdrew from the gruelling event.
Van Biljon had overcome torrid conditions to win the eighth stage in his category on Saturday, climbing to third overall ahead of the rest day at the midweek stage of the race.
He joined fellow South African Glen Grundy on a bike, and the all-South African car teams of Johan van Staden and Mike Lawrenson, and Duncan Vos and Robert Howie, on the sidelines. The three other vehicles had pulled out of the race during the first week.
Meanwhile, Riaan van Niekerk clung to 14th position overall in the bikes division, after completing the stage in 21st place, and Darryl Curtis dropped back one spot to 17th after finishing 31st on Monday.
Brett Cummings shifted further up the field as he continued his late charge, climbing another five places in the standings to 60th after taking 48th for the stage. – Sapa