De Villiers went into the 14th stage with only a two-minute lead over Volkswagen teammate Mark Miller of the United States, and secured the victory by finishing first from Cordoba across the pampas into Buenos Aires, where the first Dakar Rally in South America started two weeks ago.
After more than 48 hours of racing more than 5,600 through Argentina and Chile, over the Andes and through the Atacama Desert, de Villiers and German co-pilot Dirk von Zitzewitz ended up winning by just under 9 minutes ahead of Miller, who placed sixth on the stage.
"This is an incredible feeling," de Villiers said. "Even though I've ended up winning the Dakar that was not staged in Africa, which is home to me, it was definitely a genuine Dakar Rally, and the toughest edition I've ever contested."
NASCAR driver Robby Gordon of the United States, who's Hummer suffered a puncture on Saturday, was third, 1 hour, 47 minutes behind.
Marc Coma of Spain cruised to his second motorbike title in three years. Coma led by more than 20 minutes after the opening stage two weeks ago, and extended it to nearly 90 over previous titleholder Cyril Despres of France.
De Villiers' victory also marked the first by a diesel-powered car, and was VW's second title -- first since 1980 -- ending Mitsubishi rule since 2001.
Of a possible 13 stage wins, VW won 10, with de Villiers claiming four and Carlos Sainz six.
De Villiers regained the overall lead on Thursday after dominating teammate Sainz, the two-time world rally champion, crashed. Winning that 12th stage was the key to victory, the 36-year-old South African said. He took it easy on Friday but covered the 141 miles across the flat and wind-swept pampas in 1:35:43, just 2 seconds better than Leonid Novitskiy of Russia, and 17 seconds ahead of Krzysztof Holowczyc of Poland.
"I'm filled with incredible joy and relief," Von Zitzewitz said. "Up to the very end there was enormous pressure on us, and I only believed in our success after we'd completed the last special stage."
After numerous South African championships in the 1990s, de Villiers was an impressive fifth in his Dakar debut in 2003. He followed with a seventh ('04), fourth ('05), second in his first race with Von Zitzewitz ('06) and 11th ('07). In the meantime, he won several Moroccan Rallies, and was competitive in every other event. He was runner-up in the 2007 cross country World Cup.
The 31st Dakar was held in South America after the 2008 race was canceled because of fears of terrorist attacks in Mauritania.
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