The Toyota driver completed the 405km timed section between Arequipa and Tacna in three hours 38 minutes and 49 seconds, almost two minutes ahead of the Mini of Frenchman Stephane Peterhansel on Thursday, reports Xinhua news agency.
Poland's Jakub Przygonski was third, eight minutes and 32 seconds behind the leader.
"I'm quite happy today," Al-Attiyah said. "We won the stage but there is perhaps still a faster car out there. There's still a long way to go."
Al-Attiyah leads second-placed Peterhansel by almost nine minutes in the overall standings, with Spain's Nani Roma third, 20 minutes and 51 seconds off the pace.
Meanwhile American Ricky Brabec took the lead in the motorbike section after beating Austrian Matthius Walkner by more than six minutes in Thursday's stage. Chile's Pablo Quintanilla is second overall and Australia's Toby Price third.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)