The Qatari had accused organisers of "killing the race early" with a decision to allow cars using renewable energy - which includes the electric hybrid Audis - more power from stage five.
The World Rally-Raid Committee decided the Equivalence of Technology tweak after an analysis of data from vehicles in the first three stages.
Al-Attiyah, a four-times Dakar winner, still chalked up his second stage win of this year's event after taking control of the 373km special loop around Ha'il.
He finished one minute 57 seconds clear of Spaniard Carlos Sainz (60), whose Audi teammate and 14-times Dakar winner Stephane Peterhansel (57) was third.
"We try really to push like crazy. We take a lot of risks after the decision of yesterday. The other teams have more horsepower but OK, I’m happy to finish today without any problems," said the Qatari.
Sainz said it had been a tough stage.
"I think I injured a little bit my neck in one compression. I hope it’s not too bad tomorrow," he said of the desert conditions. "We hope we can carry on and go to the end. It’s still a long way. We need to keep pushing".
Al-Attiyah is now 22 minutes and 36 seconds clear of Peterhansel in the overall standings with Saudi Arabia's Yazeed Al Rajhi (41) dropping to third and three-times Dakar winner Sainz fourth.
Nine-times world rally champion Sebastien Loeb (48) rolled his car around 100km from the finish and lost almost 15 minutes. The Frenchman is out of the top 10 and nearly two hours behind the leader.
In the motorcycle category, French rider Adrien van Beveren (32) won the stage ahead of Chilean Jose Ignacio Cornejo (28) and Australian Toby Price (35).
Wednesday's winner Joan Barreda (39) suffered a fall 30km from the end, banging his head on the ground but completed the stage after Price and others stopped to help.
American Skyler Howes took over at the top for Husqvarna, two minutes seven seconds clear of Price with Argentina's Kevin Benavides third.
