On Sunday, in the longest special stage of the race and having to contend with high altitude and rain after a stopover without mechanical assistance, the 13-times champion known as 'Mr Dakar' secured the 40th stage win of his career.
It was also his second stage win of the current rally but, with Monday's timed stage leading into Argentina cancelled due to weather conditions, he knew it was unlikely to make much of a difference.
"At least we didn't run into trouble, which is good," he said of the 498-km special stage from the salt flats of Uyuni to Tupiza.
"I'm not back in the game, because we're talking hours of time difference and I just got a few minutes back," added Peterhansel.
"Gaining two minutes on Nasser Al-Attiyah won't bring us back into the game. It's a pity that tomorrow's stage has been cancelled because we needed every opportunity we could get our hands on to claw back time."
Sainz was fifth on the stage, seven minutes and four seconds slower than Peterhansel, but remained an hour and six minutes clear of Qatari challenger Al-Attiyah in a Toyota.
Peterhansel was an hour and 13 minutes off the lead.
"We'll try to do our best in the next six days," said Al-Attiyah, a two-times Dakar winner. "If Carlos makes a mistake, we can catch him. But one hour... it's going to be difficult."
In the motorcycle category, French Yamaha rider Adrien van Beveren remained in the lead but with a reduced advantage after a stage won by compatriot Antoine Meo on a KTM.
Van Beveren is now just 22 seconds clear of Argentina's Kevin Benavides.
The rally proper will resume on Tuesday for a stage between Salta and Belen.
The Dakar ends in Cordoba, Argentina, on Jan 20.
(Reporting by Alan Baldwin in London, editing by Clare Fallon)
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