Ricky Brabec won the motorbike section of the 477 kilometre stage to Riyadh.
Bobby Patton, co-owner of the Los Angeles Dodgers baseball team, crashed out of his first Dakar after four kilometres. The race news service reported that the accident left "his co-pilot with back and torso injuries."
Frenchman Peterhansel finished one minute 35 seconds ahead of Spaniard Sainz.
Defending champion Nasser Al-Attiyah of Qatar was third in his Toyota, 3min 22sec off the lead, with Saudi driver Yazeed Al Rajhi warmly greeted by fans as he finished fourth in another Toyota a further 3min 20sec back.
Foremr Formula One champion Fernando Alonso was sixth in his Toyota, 7min 56sec behind Peterhansel.
Sainz increased his lead in the overall standings to 7min 46sec over Al-Attiyah. Peterhansel is third, 16min 18sec behind Sainz. Two-time Formula One champion Alonso is 16th, more than three hours off the pace.
The stage started over fast, flat sands but there were dunes later on.
"It's a very fast stage," 13-time Dakar winner Peterhansel said as he paused at the 300-kilometre neutralised point. "Some parts are really quick on the sand and there are also dunes."
"Sometimes the dunes are caved in on the other side," he added. "So when you approach it quickly, you do a jump which can be difficult to handle on landing!"
Saudi entrant Al Rajhi continued his strong showing despite mechanical difficulties.
"I am happy," he said. "I'm from Riyadh. I have a lot of fans here and I enjoyed it a lot so thanks to them for coming."
"Today was not an easy day. After the start we had a leak of oil and we were scared because there was a crack and I was scared all the oil would leak out. But taking care and taking it easy was the most important."
Brabec grabbed his second stage victory in the motorbikes, finishing 1min 34sec ahead of Honda team-mate Spaniard Joan Bareda. Austrian KTM rider Matthias Walkner was third at 2min 45sec.
"It was a long stage," Brabec said. "It was a big one, the first real stage of 100 per cent sand. I'm just happy to be here and to be leader in the general standings."
Saturday is a rest day.
"We deserve some rest," said Brabec who leads Chilean Pablo Quintanilla of Husqvarna by 20min 56sec in the overall standings at the half-way stage.