Wednesday's Neom - Al-'Ula stage included the marathon's longest timed test so far at 453km, which was split by an 80km neutralised zone and was completed by Peterhansel in just over four hours.
The 13-time Dakar champion was sixth in the starting order, but his X-raid Mini buggy was the third car to arrive at the finish line and had clocked the fastest time at all but the first waypoint.
Squadmate Sainz looked on course to minimise the damage from having to open the road, but gave up over four minutes in the final 100 kilometres of the test.
This means Toyota driver Al-Attiyah, who had entered the day as Sainz's closest rival and was a close second to Peterhansel through the stage, now trails the leader by just three minutes.
Al-Attiyah had received a three-minute penalty after Tuesday's stage as he was adjudged to have impeded Sainz.
#412 Red Bull Off-Road Team USA OT3: Mitchell Guthrie, Ola Floene
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