The Frenchman now leads team mate and compatriot Cyril Despres, the overnight leader on Sunday, by three minutes and 11 seconds.
"It was complicated because there were a lot of dunes again," he said. "The navigation was a little bit easier this morning because the bikers started first this morning.
"They navigated really well so most of the time we followed the lines of the bikers... we did not drive the stage on full attack, just with a good speed."
Al-Attiyah, who also won Saturday's opening stage, moved up from fifth overall to third and 7:43 off the lead despite losing around three minutes with a flat tyre.
"We needed to push, but not really crazily. It was not a big push, because the road really isn’t easy and very dangerous in places," he said.
"It's good, except for yesterday when we opened (the road)which was very difficult for us because there were no lines, but I think we are in a good way now."
Nine-times world rally champion Sebastian Loeb, also in a Peugeot, dropped to fourth after finishing more than eight and a half minutes behind the Qatari.
It was a bad day for Spanish driver Nani Roma, a Dakar winner on motorcycle and car, who rolled his Mini near the finish and suffered head and neck injuries.
Roma finished the stage, with co-driver Alex Haro largely unhurt, but was flown by helicopter to a nearby airport for medical checks in Lima.
Britain's Sam Sunderland, the Dubai-based defending champion, went back to the top of the motorcycle standings after Honda's overnight leader Joan Barreda lost his way and dropped almost 28 minutes.
Sunderland won the stage, his second victory for KTM in three days, to lead Honda's Argentine rider Kevin Benavides by four minutes and 38 seconds.
Tuesday's fourth stage starts and ends in San Juan de Marcona after a 330km special stage that includes one of the longest sandy sections in the event's history.
(Reporting by Alan Baldwin in London, editing by Pritha Sarkar)
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