Gordon was 22 seconds ahead of Guerlain Chicherit of France in the cars category, while Peterhansel finished nearly 14 minutes off the pace.
Peterhansel is still expected to win his 11th Dakar title barring any mishap, as he leads the overall car standings by 44 minutes, 38 seconds ahead of Giniel de Villieres of South Africa. Other competitors are more than an hour behind.
The rally finishes Saturday in the Chilean capital of Santiago.
"We didn't take any risks at all and we only lost a few minutes, but we managed to protect our lead this way," Peterhansel said.
"There were some impressive dunes, but rather than risking getting stuck on them, we preferred to go either right or left around them and then get back on track afterward."
Peterhansel spoke cautiously, knowing he still might face problems.
"It will be simpler tomorrow because it is less long than today," he said. "I think we still have a lead of around 45 minutes, so we're going to carry on taking it easy. But there's no sign of relief yet. We know how it goes: something could still happen right up until you cross the finishing line."
In motorbikes, defending champion Cyril Despres closed in on his fifth Dakar title. Despres leads KTM teammate Francisco Lopez of Chile by 8:15 in the overall, and is 14:14 up on another KTM rider Ruben Faria of Portugal.
"Since I ate quite a bit of dust in the morning, I preferred to make sure and take it easy," Despres said. "As for celebrating, we still have 220 kilometers to the bivouac today (Friday) and with 690 kilometers tomorrow, it's not going to be a walk in the park."
Lopez won Friday's stage, with Despres 5:25 behind.