Having won the title six times on bikes, this was the Frenchman's fourth success in the car category and his first for Mini, and he was rarely in trouble from start to finish.
He got his bad fortune out of the way two stages ago as he suffered punctures and got stuck in sand dunes, and it was plain sailing from then on as he finished 41 minutes and 56 seconds ahead of Mini team-mate Nani Roma.
Roma may have made more of a fist of things had he not got stuck in the dunes yesterday, while 10th-placed Krzysztof Holowczyc may also have been in the shake-up had he not suffered severe mechanical problems midway through the second week.
Leonid Novitskiy made it three Minis in the top four, and only Toyota's Giniel de Villiers prevented an all-Mini podium by taking third, some hour and 13 minutes behind Peterhansel.
"My finest victory will always be my first win in the motorcycle category, but this one has something special to it," Peterhansel told the media afterwards.
His old motorbike category was won by Cyril Despres, who came through the final stage unscathed to see off nearest challenger Marc Coma.
It was Despres' fourth title on his KTM, crossing the line with a total time of 43 hours, 28 minutes and 11 seconds. He was 53 minutes and 20 seconds ahead of Coma and an hour and 11 minutes clear of third-placed Helder Rodrigues.