The 2002 event winner began the final 282 km competitive section with a commanding 69-minute lead over his nearest rival, the UAE's Khalifa Al-Motaiwi. He eventually beat the BMW driver by a margin of 1h 14m 13s.
Meanwhile South Africa's Alfie Cox managed a fifth place overall in the motorcycle category after a terrible start to the first event in the 2004 Cross Country World Cup Series.
"I would have preferred a podium finish, but I am totally satisfied with what I achieved. It is two years since I have last been to the Rally of Tunisia.
"Last year I could not compete in the World Cup as a result of my accident in the Dakar. Some of the navigation was unique to this race and I have yet again learnt a lot. I hope to do most of the World Cup events this year and be very well prepared for the 2005 Dakar," commented Cox at the stage finish.
Defending Cross Country World Cup champion Cyril Despres took overall honours in the motorcycle category ahead of Spain's Marc Coma and his fellow countryman Richard Sainct. Another Spaniard Esedré Esteve Pujol finished ahead of Cox.
Back to the cars, and winner Peterhansel commented:
"Last year's Rally of Tunisia was my third consecutive disappointment and now, 12 months later, this is my third win in three major rallies.
"It is a great feeling. This was not the hardest of races for me, because after two days I had a big advantage. But it is easy to lose concentration when you are not pushing to the limit."
Japanese team mate Hiroshi Masuoka and French co-driver Gilles Picard shadowed Peterhansel to the finish in the second Mitsubishi Pajero Evolution. They lost their chance of taking a podium placing after clutch problems on the first stage last week and finished second overall through the final stage.
The next event will be the Orpi Rally of Morocco at the start of June. Stéphane Peterhansel and Jean-Paul Cottret will be joined by a second yet-to-be-announced driver.
1. Stéphane Peterhansel (F)/Jean-Paul Cottret (F) Mitsubishi Pajero/Montero Evolution 21h 02m 49s
2. Khalifa Al-Mutaiwi (UAE)/Alain Guehennec (F) BMW X5 Rallye-Raid 22h 17m 02s
3. Stéphane Henrard (B)/Alain Low (B) Volkswagen Tarek 22h 40m 06s
4. Jose-Luis Monterde (E)/Rafael Tornabell (E) Mitsubishi Pajero/Montero 23h 33m 13s
5. Georges Lansac (F)/ Jean-Robert Jacquemard (F) Pro Truck 23h 44m 30s
6. Dominique Housieaux (F)/Jean-Marie Lurquin (B) Mitsubishi Pajero/Montero 23h 50m 14s