The stage victory was the first this year for five-times Dakar winner Al-Attiyah, whose Prodrive Hunter finished one minute and 51 seconds ahead of French Toyota driver Guerlain Chicherit.
Al-Rajhi was fourth fastest over the sand dunes on the 118km stage from Al-Hofuf to Shubaytah that saw several top contenders ease off to gain a later start on Thursday with tracks to follow.
The Saudi retained the overall lead, nine minutes and three seconds clear of Al-Attiyah with Audi's Carlos Sainz dropping to third.
"There was no strategy on my part. I wanted to win the stage no matter what they have in store for us tomorrow," said Al-Attiyah.
Al-Attiyah has now won Dakar stages with seven different constructors over the course of his career, Wednesday being the Qatari's first in a Prodrive Hunter.
Rival and nine-times world rally champion Sebastien Loeb, Tuesday's winner, lost more than 21 minutes to Al-Attiyah including a 15-minute penalty for deliberately missing a waypoint.
The Frenchman dropped to ninth overall from third, 43 minutes off the lead.
"Nasser and I are following different strategies. He wants to start early and feels confident. I wouldn't have done that. We're not equally knowledgeable about the desert, he's in his element," said Loeb.
"I opted for following the tracks (on Thursday). That's my choice. We lost big time today in the hope of winning big time tomorrow."
The 48-hour Chrono Stage will see contenders race through the kingdom's Empty Quarter with marathon stage restrictions and the motorbikes running a different route.
"We stopped for a while. I don't know whether it was the right strategy, we'll see in two days, but we didn't want to be at the front," said Sainz.
In the motorcycle category, Botswana's Ross Branch returned to the top in a stage won by Chilean Pablo Quintanilla on a Honda.
Branch leads Chile's Jose Ignacio Cornejo by one minute and 14 seconds with American Ricky Brabec third.
