"Jakub (Przygonski) was pushing but he doesn't have anything to lose. We did a good job from start-to-finish," said Al Attiyah.
"Some place, we've been careful to find the road. Everything disappears from the wind. We're quite happy. We won again. It was more sandy. We'll see how it goes," the three-time Dakar Rally champion added.
The day's Al Kharsaah selective section was the longest of the event at 340.28km.
The track headed south towards the Inland Sea, before turning north-west back through the central deserts to finish in the north-west of the country.
Fierce T3 battle
A fierce battle raged in T3 behind leader Austin Jones, who started the day with a 19-minute advantage.
Saleh Al Saif, Ahmed Al Kuwari, Kees Koolen, Mubarak Al Hajri, Fedor Vorobyev and Khalid Al Mohannadi were locked in a six-way tussle for the stage win.
Destroyed by fire
Meanwhile, Gonzalo Guayasamin's Polaris was destroyed by fire on special stage three.
Day four is split into two parts with the opening Al Shahaniyah selective section of 219.79km starting from the Dukhan road and heading north, before turning south along the west coast to finish close to the Umm Bab highway.