The outcome could have been much worse, however, with the rider going under the car.
Peterhansel, the reigning champion and a six-times winner on motorcycles before switching to cars and winning another six times, waited with the KTM rider until the medical helicopter arrived.
"Everybody was completely lost," said the Frenchman, who finished the stage six minutes and 45 seconds behind overnight leader Loeb but was given back 14 minutes and 13 seconds by organisers.
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Loeb had initially been declared stage winner.
"The biker was in reverse. When he saw me, he braked, and he crashed and I stopped on him. I saw that his leg was broken but he was still conscious. We stayed for about 15 or 20 minutes with him and waited for the medical helicopter," said Peterhansel.
"Afterwards, it was really complicated to restart, to drive with a good speed. Not an easy day."
Peterhansel now leads Loeb by five minutes, 50 seconds with two stages remaining before the finish in Buenos Aires on Saturday.
In the motorcycle category, Britain's Sam Sunderland has a half hour advantage over Austrian Matthias Walkner with Spaniard Joan Barreda taking his third stage win of this year's competition.
"Everybody got lost around 40 km and then I saw Sam and he also didn't know where we had to go. But in the end, he did a pretty good job all day in front," said Walkner.
Chilean Pablo Quintanilla, who had been in second place, retired after a fall some 400km into the special stage.
(Reporting by Alan Baldwin in London, editing by Peter Rutherford)
