Peterhansel outpaced fellow Mini buggy driver Sainz by a minute and 21 seconds over the 477-kilometre timed special between Ha'il and Riyadh, with the day's route dominated by sand dunes.
Toyota's reigning champion Nasser Al-Attiyah completed a familiar top three on the day as he stayed within a minute of Peterhansel and Sainz during the first half of the stage before ultimately dropping to three minutes off the pace by the finish.
Al-Attiyah now trails Sainz by just under eight minutes in the general classification, while Peterhansel is a further eight and a half minutes back.
Another Toyota driver Yazeed Al-Rajhi was best of the rest behind the three Dakar champions for a third day straight, as he gave up six and a half minutes relative to Peterhansel.
And though he sits over half an hour behind Sainz overall, the Friday result has allowed local hero Al-Rajhi to pull clear of Orlando Terranova for fourth place heading into the rest day.
Mini driver Terranova, who had led the rally after day two, surrendered nearly a quarter of an hour through the sixth stage.
He remains in fifth place, ahead of Century driver Mathieu Serradori, who continues to hold off the Toyota Gazoo entries of Giniel de Villiers and Bernhard ten Brinke.
Two-time Formula 1 champion Fernando Alonso showed top-five pace for much of the stage, but was ultimately shuffled down to sixth place on the day by Serradori in the final 50km.
Alonso is over three hours behind Sainz overall following his stop for damage repairs during stage two.
The 2020 Dakar Rally will resume on Sunday, as the peloton will head to Wadi ad-Dawasri from Riyadh and contest the marathon's longest timed special at 546km.
General classification (top 10):
|Pos.||#||Driver / Co-driver||Car||Time||Gap|
|3||302|| Stephane Peterhansel |
Giniel de Villiers
Bernhard ten Brinke
SxS: Lopez, Currie make a break for it
Gerard Farres won the sixth stage in the SxS class, but it's reigning champion Francisco Lopez and Casey Currie who look poised to battle for overall fictory.
Lopez finished a minute behind Farres - who is more than four hours down in the overall classification - to leapfrog both Currie and overnight leader Sergey Karyakin.
Currie now trails Lopez by 10 minutes, while Karyakin is another 20 down, but remains in third place due to Austin Jones losing more than an hour on Friday.
Fourth-placed Jose Antonio Hinojo Lopez is six minutes behind Karyakin, while Mitch Guthrie, the last driver within an hour of Lopez, continues to head the Red Bull Overdrive contingent in fifth.
Trucks: Nikolaev out but Kamaz in control
Eduard Nikolaev has exited the 2020 Dakar Rally due to persistent mechanical issues with his truck, meaning the Trucks class will officially now crown a new champion following three consecutive wins for the Russian.
But fellow Kamaz driver Andrey Karginov looks likeliest to inherit the mantle, having outpaced squadmate Anton Shibalov in stage six to take his lead in the marathon to nearly 20 minutes over Shibalov.
Maz driver Siarhei Viazovich is the only other competitor within an hour of the Kamaz pair, and sits 36 minutes behind Karginov after Friday's running.