Roma in command as Peterhansel suffers
Mini's driver Nani Joan Roma (C) of Spain and co-driver Michel Perin compete during the Dakar Rally 2014 Stage 1 between Rosario and San Luis, Argentina, on January 5, 2014
Frenchman Peterhansel began the day in the overall lead following his victory in Monday's second stage, but punctured six times as he came home in 28th place, more than 28 minutes down on Roma.
In the overall standings, Roma leads a trio of Mini drivers with Argentine Orlando Terranova second and Nasser Al-Attiyah of Qatar in third.
Peterhansel is down in fifth place overall but is 24min 08sec behind Roma.
And the 11-time former winner (six times in the moto section and five times in cars) admitted he had not enjoyed the 301km timed section from San Rafael to San Juan.
"I've never known a Dakar stage like this one," said a frustrated Peterhansel.
"It was a nightmare today. We punctured six times! Unfortunately we opened on the course and we paid for it.
"On the first I hit a big rock, that's my fault, but then we were the first to go out and we found ourselves completely off-piste in very tall vegetation thanks to a last-gasp swerve due to bad weather and mud.
"And when we got out of that, we had three slow punctures out of four wheels, certainly due to the pines in the sides of the wheels.
"Unfortunately, as we were the first car, we cleared the track for the rest behind. We were thrown into the lion's den but I can't see how we could have done anything differently.
"We couldn't have imagined that in clearing a path in the vegetation we'd get three punctures out of four."
In the motorcycle section Spaniard Joan Barreda on a Honda increased his overall lead by winning the third stage, a 292km timed special.
Frenchman Cyril Despres on a Yamaha came in second with Spain's Marc Coma third on a KTM.
Those three remain in those exact positions in the overall standings.