Mini driver Peterhansel, who won six motorcycle Dakars for Yamaha in the Nineties, added a fourth cars title as the leading GC drivers coasted home safely, with team-mate Nani Roma finishing second overall and Giniel de Villiers of Toyota third.
It was Peterhansel's first triumph in the Dakar since it arrived in South America due to security concerns. His previous wins in the cars section - all for Mitsubishi - were in 2004, 2005 and 2007.
American Hummer driver Robby Gordon claimed the 29km special on the final stage between Pisco and Lima in Peru in a time of 22 minutes 43 seconds.
Mini's Ricardo Leal dos Santos of Portugal was second, 21s back, with Pole Krzysztof Holowczyc third (38s).
South African De Villiers was fourth, Spaniard Roma eighth and Peterhansel 10th.
"When you think of how hard it is to win a Dakar, it's incredible that I've been able to win ten of them," said the champion.
"It's been a long time, I've been waiting for five years to win again! To take the victory in South America is a huge relief, it ranks among my best triumphs. Moreover, the race was very close during the first week and there was always a lot of pressure.
"Beating this record is going to be difficult... for the others. This race is stressful, exciting and fascinating, and it's also very rewarding at the end.
"My finest victory will always be my first win in the motorcycle category, but this one has something special to it. I was starting to doubt myself, to think I was growing too old for this, that I'd lost it or that I wasn't made for South America... and in the end everything turned out fine.
"But I still have a blue bandana from my motorcycling period. I didn't tell anyone, but I kept it in my pocket throughout the entire rally. It's the story of the comeback of the blue bandana."
De Villiers was delighted to be the best non-Mini driver.
"Our aim was to crack the Top 5, since we knew we were at a disadvantage with regard to the Minis," he said.
"Our car was designed based on the future rules, so we had a power deficit compared with them, especially on sandy surfaces. But our car was completely reliable and our team did a fantastic job.
"This is an excellent result, finishing on the podium on our first try tastes like a win. The rules are going to change next year, so we'll be even closer and the battle will be awesome. There's no doubt we'll try and win next year."