De Villiers, who twice benefited after previous leaders dropped out during the two-week event, finished the 227 kms timed section of the stage from Cordoba to Buenos Aires in one hour 35 minutes 43 seconds.
He finished two seconds ahead of Russian Leonid Novitsky.
"I was so nervous in the last kilometres," De Villiers told reporters. "I kept looking at how many kilometres we still had to go. But I must say this is an incredible feeling."
De Villiers was handed the lead for the first time during the sixth stage when Qatari Nasser Al Attiyah was disqualified for failing to follow the official route.
He was overtaken the following day by Carlos Sainz but regained the lead on Thursday when the Spaniard crashed out.
De Villiers finished eight minutes 59 seconds ahead of Volkswagen team mate Mark Miller of the United States in the overall standings and one hour 46 minutes ahead of another American Robby Gordon.
The race was moved to Argentina and Chile this year from its traditional venue in Africa because of security fears in Mauritania which forced the cancellation of last year's event.
But it retained its deadly reputation when French motorcyclist Pascal Terry was found dead on Jan. 7, three days after going missing during the second stage. He was the 26th competitor to die in the race's 31-year history.
British competitors Paul Green and Matthew Harrison both suffered serious injuries after their car overturned during the first stage and Spanish biker Cristobal Guerrero was left in a coma after an accident during the 10th stage.
Spain's Marc Coma, champion in 2006, comfortably won the motorcycle race for a second time after finishing third in Saturday's final stage, won by Portugal's Helder Rodrigues.
Coma finished one hour 25 minutes 38 seconds ahead of former champion Cyril Despres in the overall standings with David Fretigne third.
"Although it was a tough race, which required a lot of work and suffering, I enjoyed it a lot," Coma said. (Editing by John Mehaffey)
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