Audi's Carlos Sainz, a triple Dakar winner, led the virtual rankings in the car category while defending champion Nasser Al-Attiyah dropped back to third after the first leg of the marathon stage in the kingdom's Empty Quarter.
Drivers started the day facing a 549km challenge over two days, with an obligatory stop at 4 pm local time, but Al-Rajhi crashed after just 51km.
The Dakar website reported that the Overdrive Toyota hit a bump or clump of grass and barrel-rolled, suffering heavy damage.
The car was taken back to the start of the sixth stage with no guarantee of being able to continue on Sunday, the seventh stage after Saturday's rest day.
Al-Rajhi had started the day nine minutes and three seconds clear of Qatar's Al-Attiyah.
Sainz looked well-placed for a 43rd career stage victory after he got ahead of Al-Attiyah's Prodrive Hunter early on in the soft sand and dunes.
The Spaniard was the 17th starter, after strategically slowing on Wednesday, and ended the day four and half minutes clear of teammate Mattias Ekstrom.
Audi's Stephane Peterhansel, a record 14 times Dakar winner, suffered problems with the hydraulics and power steering, however, and lost more than two hours.
"We had a puncture and the hydraulic jack system started playing up. We don’t have a hand jack so we don’t know how we’re going to change the wheel," he reported.
"With the damage to the hydraulic system, I’ve lost the power steering and I don’t know how we’re going to manage to pull through."
In the motorcycle category, Chilean Honda rider and Wednesday's stage winner Pablo Quintanilla lost an hour and 40 minutes after running dry before the first refuelling point.
American Ricky Brabec was in the lead position, two minutes and 48 seconds clear of Botswana's Ross Branch.
