Peterhansel, who led by one minute 57 seconds overnight, ended the day one minute 38 seconds behind the nine times world rally champion, who won his third stage of this year's event.
It might have been more if Loeb, who started after his team mate, had not suffered a puncture on the Argentine side of the border.
"I tried really hard because today was a stage like the ones I like, with some fast roads, whereas tomorrow is more desert-like with dunes," said Loeb.
"I wanted to try to make a gap today but finally I had a puncture on the last part of the stage so I lost a few minutes to change the wheel," he added.
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"At the moment the fight seems to be between me and Stephane, but I think the two next days will be very, very tough and anything can happen there."
The rally, which finishes in Buenos Aires on Saturday, is famed as one of the toughest endurance challenges in motorsport.
Previously a gruelling race from Paris across the Sahara to the Senegalese capital, it switched to South America in 2009 for security reasons.
In the motorcycle category, British rider Sam Sunderland increased his overall lead after finishing third in the stage won by Spain's Joan Barreda.
Sunderland now leads Chile's Pablo Quintanilla by nearly 21 minutes.
"It was really, really wet and difficult to pass in some places. I stopped a few times to change my goggles and change my gloves and silly things, just because it was too much," he said.
"I couldn't see the road book, I couldn't see where I was going," added Sunderland, who said he had completed the last 100km with no rear brake.
(Reporting by Alan Baldwin in London, editing by Ken Ferris)
