Peterhansel, nicknamed "Mr Dakar", has now won the car category eight times, having also won the motorcycle category six times.
The 55-year-old MINI driver, aided by co-pilot Edouard Boulanger, finished ahead of Qatari Nasser al-Attiyah (Toyota), with Spain's Carlos Sainz rounding out the podium in another MINI.
Peterhansel's victory came shortly after news that French motorcyclist Pierre Cherpin had died from his injuries after a fall, becoming the race's first fatality this year.
Argentina's Kevin Benavides won the motorbike category, leading home defending champion Ricky Brabec of the United States in a first Honda 1-2 since 1987.
Briton Sam Sunderland, the 2017 champion, finished third.
Benavides, who broke his nose in a crash on the fifth stage that saw his helmet shattered, became the first South American to win the category, calling it "absolutely crazy".
"I went at 110 percent, but now it's true: I've won the Dakar - I'm so, so happy! I did some mistakes, for sure. I think it's impossible to do a perfect Dakar," he said.
"The important thing is to always continue, to stay calm and focused day by day and to work hard day by day."
Brabec admitted to feeling "pretty bummed" at not defending his title, but added that "number two will work".
"I didn't even know that Honda had already won a one and two finish. I wasn't even born in 1987! It's cool to go one and two again."
