The Frenchman, nicknamed 'Mr Dakar' for his success on two wheels and four, had been in fourth place at the start of the stage around the southern city of Pisco.
Organisers said Peterhansel's X-Raid Mini co-driver David Castera was suffering back pain after the accident, 26km into the 312km timed stage.
Qatar's Nasser Al-Attiyah leads the endurance rally, which ends in Lima on Thursday, and is on course to win for the third time.
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(Reporting by Alan Baldwin, editing by Christian Radnedge)
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