"We're quite happy to take this win. This wasn't an easy race with lots of navigation. Today we have three flat tyres. It wasn't easy for the tyres here," Al Attiyah said.
The three-time Dakar Rally champion dwelled further, "The last 50km, we lost the pressure in the tyres and we reached the finish line with two punctures. But I won the stage and I lead the championship, so we're happy."
Yazeed Al Rajhi and Michael Orr claimed one stage win and finished the last timed section of 254.58km in third place from first on the road to confirm the runner-up spot in the second of the Overdrive Toyota Hiluxes.
They also suffered tyre wear on the abrasive rocky terrain and were then handed a 10-minute time penalty for leaving a destroyed wheel and tyre in the desert.
"We had a small tyre problem," said Al Rajhi, who reached Losail with rear left panel damage as a result.
"The tyre stripped out. That was all, except for one puncture. We stopped to change it. Then we took it easy, because Kuba (Przygonski) was at the front and he continued the stage with puncture and I followed him. I'm happy with this position. That was our plan. Let's see what happens in the future."
Poland's Jakub Przygonski and German navigator Timo Gottschalk battled back from a near two-hour time loss on day two to secure the final podium place on their first appearance together in a Toyota.
Broken steering and punctures had pushed the 2018 FIA World Cup champion down to seventh position at the start of day three, but the Pole found an impressive rhythm for the remainder of the rally and reached the end of the last stage at Ash Shafallahiyah with the second quickest time, he too crossing the finish line with two flat tyres.