Peterhansel, who had already won the Dakar and Tunisia rallies this season, began the final two stages between Oued Chebika and Agadir with a 26m 30s advantage over his nearest rival Jean-Louis Schlesser and went on to win the event for the first time in a car by 23m 36s.
The success also marked Mitsubishi's first victory in the five-year history of the NPO-organised event in Morocco and gave Peterhansel the outright lead in the FIA World Cup Drivers' Championship.
"This was a perfect race for me," said Peterhansel. "This is my fourth successive win and I feel very happy. Both Jean-Paul and I were confident this morning. We were relaxed and drove slowly to make sure we had no problems."
Defending FIA World Cup champion Carlos Sousa and his Andorra-based co-driver Henri Magne finished third overall in the second Mitsubishi Pajero/Montero Evolution, despite coming under pressure from Volkswagen's Jutta Kleinschmidt on the final stage.
Former Mitsubishi driver Kleinschmidt closed to within 58 seconds of Sousa after beating him by over four minutes in the sixth section.
"I lost time to Jutta on the first stage and needed to push a little in the second one," said Sousa. "It was a nice day and I was pleased to finish third here. It was a challenging rally, but a podium place was what I wanted."
Germany's Andrea Mayer and co-driver Andreas Schulz completed their second competitive appearance of the season in 10th position in a Mitsubishi L200 Pick-Up, despite two time-consuming incidents earlier in the week where Schulz was forced to repair a broken rear wheel knuckle.
They also suffered minor electrical problems today and a replacement battery was fitted at the assistance point.
Yesterday's final selective offered two competitive sections; the first 179 kms track headed from Tan Tan to a finish at Sidi Ifni, while the second 60 kms section began on the beach at Aglou and finished in the fishing village of Tifnit.
The next round of the 2004 FIA Cross Country Rally World Cup takes place in Spain in July. The event is also a round of the FIA European Baja Cup for Drivers.
Meanwhile, in the bikes section South Africa's Alfie Cox, racing for the KTM Factory Team, finished eighth overall after he was fourth and second respectively in yesterday's two stages.
First and second places overall went to Spain's Isidre Esteve Pujol and Mark Coma, ahead of Frenchman Cyril Despres of France. The first 10 positions were taken by KTMs.
"I had a good run today, and finished fourth in first special stage," Cox said afterwards.
"We then continued to the second special stage where I secured a second place. The eighth place overall is actually quite good in my opinion, if you take into account that I lost so much time when I gave the wheel Cyril.
"My ankle is sore, but it held up very well, although it hurt often, I nursed it to the finish."
Final positions - cars
1. Stéphane Peterhansel (F)/Jean-Paul Cottret (F), Mitsubishi Pajero/Montero Evolution, 16h 58m 07s
2. Jean-Louis Schlesser (F)/Francois Borsotto (F) ,Schlesser-Ford DSC12, 17h 21m 43s
3. Carlos Sousa (P)/Henri Magne (AND), Mitsubishi Pajero/Montero Evolution, 17h 50m 07s
4. Jutta Kleinschmidt (D)/Bobby Willis (GB), Volkswagen Touareg, 17h 51m 05s
5. Dominique Housieaux (F)/Loic Fagot (F), Mitsubishi Pajero/Montero, 18h 40m 23s
2004 FIA Cross-Country World Cup Drivers' Championship
1. Stéphane Peterhansel (F) 90 pts
2. Khalifa Al-Motaiwi (UAE) 64 pts
3. Carlos Sousa (P) 51 pts
4. Jean-Louis Schlesser (F) 33 pts