Success for the veteran Frenchman powered him into the overall lead to give him a massive boost in his quest for a 12th success in motorsport's toughest challenge.
The 50-year-old from Alsace lined up for the 542 kilometre timed run in Uyuni, the longest stage of the rally, eight minutes adrift of nine-time world rally champion Loeb.
But already the winner of Wednesday's fourth stage he now goes into Saturday's drive from Uyuni to Salta in Argentina at the head of the pack.
He leads Dakar debutant Loeb, who was hit by punctures and faulty electrics, by 27sec with Sainz in third at 5min 55sec in an all-Peugeot top three.
Defending Dakar champion Nasser Al-Attiyah, behind the wheel of a Mini, sits fourth, over 15min adrift.
After a stunning drive in Uyuni where he called on all his vast experience to deal with the tricky terrain, Peterhansel timed 5hrs 1min 7sec to cross the line 17sec clear of Sainz.
"It was a good day today," said the man who competed in his first Dakar in 1988, winning the first of his six overall victories on two wheels back in 1991 and taking his 11th victory in a Mini in 2013.
"I saw nobody, just sometimes I saw dust," he added.
"I did see Seb at the last 20 kilometres before the end. He had a puncture and I overtook him, but during all the day I was alone, trying to be completely focused on the track, because it was a really long stage."
Peugeot were destined for their third cleansweep of the race only for late finisher Yazeed Al-Rajhi of Saudi Arabia to grab third (at 7min 19sec) ahead of Loeb who later reflected on a "complicated day".
"I had a first puncture, then I had to do almost 80 kilometres with the accelerator blocked at full power, so I had to control it with a switch and it was really complicated to drive like that.
"Finally, I got another puncture and we had to change a second wheel."
In the bikes category, Tony Price took the day's honours on a KTM for his third stage win this year.
His teammate Matthias Walkner came in second at 1min5sec ahead of Paulo Goncalves (1min 12sec) but despite losing out the Portuguese Honda rider retained the overall lead.
Price is a little over half a minute away ahead of Saturday's seventh stage to Salta in Argentina.