Qatari driver Nasser al-Attiyah won the stage, a 375km timed special between Chilecito and San Juan in Argentina, in his Toyota with Sainz taking it easy and finishing 18 minutes behind.
Peterhansel, the defending champion and 13 times winner, was second.
"I think it’s finished now," said the Frenchman, whose hopes suffered a severe blow earlier in the rally when he lost an hour and 45 minutes last Saturday in Bolivia.
"We will try to secure second place, so we controlled the gap with Nasser today.
"I’m crossing my fingers for me but also for Carlos – we never know what can happen."
Organisers cancelled the timed stage for motorcycles and quadbikes for weather-related safety reasons.
"Having consulted the competitors grouped at Fiambala’s marathon bivouac, the race direction has taken the decision to cancel the 12th special stage for bikes and quads," a statement said.
Austrian Matthias Walkner is leading the motorcycle standings on a KTM, 32 minutes clear of Argentina's Honda rider Kevin Benavides.
The rally ends in Cordoba on Saturday.
(Reporting by Alan Baldwin in London, editing by Toby Davis)
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