The 53-year-old Qatari, driving for Prodrive, finished 1min 51sec ahead of Toyota's Guerlain Chicherit to claim his 48th stage win in the Dakar and moved second in the standings, gaining two minutes on cars leader Yazeed Al-Rajhi, who finished fourth behind Argentinian Juan Cruz Yacopini.
"There was no strategy on my part," said Al-Attiyah who will now have to open the road at the start of the '48H chrono', a new two-day stage across Thursday and Friday.
"I wanted to win the stage no matter what they have in store for us tomorrow.
"It's 600 kilometres long and I don't mind opening the road. Even if I lose time, what matters to me is finishing these 600 kilometres."
Sebastien Loeb (Prodrive) tried his luck by deliberately missing a compulsory checkpoint, a "mistake" that cost him a 15-minute penalty.
As a result, he finished 21min 13sec down the order, giving up time in the overall standings in the hope of optimising his chances in the '48H Chrono' by starting from behind.
"Nasser and I are following different strategies," said Loeb.
"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. I opted for following the tracks. That's my choice.
"We lost big time today in the hope of winning big time (tomorrow)."
- Quintanilla 'flat out' -
Ross Branch reclaimed the lead in the bikes category after Chilean rider Pablo Quintanilla dominated the dunes to win stage five.
On a short 118km special stage, Quintanilla was pushed all the way as he completed his seventh Dakar stage win, beating his Honda team-mate Adrien Van Beveren by just 37 seconds.
"After two awful days, everything fell into place," said Quintanilla.
"I went flat out. It wasn't easy because the glare of the sun made it hard to see the tracks but I went 100 percent from the first kilometre.
"It was tough, but I managed to set a fast pace and had a great stage.
"I wasn't expecting this type of soft sand because I heard it had rained in the last few days, but I had fun anyway. I had a great time on my bike."
Two-time winner Toby Price (KTM) completed the podium at 1min 39sec.
Honda's other Chilean Ignacio Cornejo had a difficult day in the saddle.
After his stage four victory on Tuesday, which had give him the overall lead, he had the difficult task of opening the special and finished 6min 11sec down on his compatriot.
That allowed Botswana's Ross Branch (Hero), who came sixth on the stage, to retake the lead in the provisional overall classification, 1min 14sec ahead of "Nacho" Cornejo.
"Opening the road in the dunes was tough," said Cornejo.
"I tried to do a good job and my teammate Ricky Brabec joined me around the kilometre 50 mark. I reckon we worked well together.
"I hope tomorrow will be better."
The American Brabec is third in the standings at 3min 47sec.
Argentine world champion Luciano Benavides (Husqvarna) was on course for a fast time before running into technical problems in the last five kilometres.
He finished the stage 4min 22sec behind Quintanilla and later said his team would be installing a new engine which will mean a 15min penalty.
The "48H Chrono" is the last big chunk of the first week of the Dakar before a rest day in Riyadh.
