It was France's Jean-Louis Schlesser, driving a Ford, who won Monday's 497km stage between Tichit and Nema, ahead of countrymen Luc Alphand, the reigning champion, and Peterhansel.
Peterhansel, in a Mitsubishi, jumped into the overall lead at the expense of overnight leader De Villiers of South Africa, and is now almost eight minutes ahead of Alphand.
"We had mixed emotions when we saw De Villiers' car on fire," admitted Peterhansel.
"Of course it's important for the overall rankings but we think he did not deserve it. He was doing his best Dakar and driving wonderfully well.
"A few kilometres further, we also had trouble of our own when we fried our clutch. We had to repair and lost 15 minutes. Standings are never set in stone in the Dakar. It's nice to be in the lead for the first time in the rally.
"But now we have to finish the next four stages. Pressure is on our side now."
Stage winner Schlesser, overall champion in 1999 and 2000, had his sights set firmly on moving into contention for the podium.
"We are only two minutes behind Nasser al-Attiyah," he said. "Well, we'll pass him tomorrow.
"I'm happy because it was a difficult stage, for instance the whole section with a lot of sand, which is not an advantage for us.
"Three days ago, Volkswagen was untouchable; I thought they were. I still believe that if they had not had problems, they could not possibly have lost.
"As far as Im concerned, I will now focus on how to get a position in the top 3. My concern is that there are still 2-3 hard days ahead on terrains where my immediate rival Nasser al-Attiyah should do better than I with his 4x4."
Stage 9 classification:
Pos Driver Make Time
1. Schlesser Schlesser 5h32:03
2. Alphand Mitsubishi + 0.13
3. Peterhansel Mitsubishi + 4:14
4. Masuoka Mitsubishi + 8:38
5. Roma Mitsubishi + 14:27
6. Al Attiyah BMW + 14:34
7. Sousa Volkswagen + 30:21
8. Kleinschmidt BMW + 31:09
9. Shmakov Buggy + 31:45
10. Miller Volkswagen + 31:52
Overall standings after stage 9 (provisional):
Pos Driver Make Time
1. Peterhansel Mitsubishi 33h23:43
2. Alphand Mitsubishi + 7:50
3. Al Attiyah BMW + 1h23:21
4. Schlesser Schlesser + 1h25:32
5. Masuoka Mitsubishi + 2h13:44
6. Miller Volkswagen + 2h14:26
7. Sousa Volkswagen + 4h11.29