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The South African, who won the race in 2009, finished second in Saturday's 13th and penultimate stage, and while he retained third place overall, he was well over an hour behind race leader Stephane Peterhansel of France.
Spaniard Nani Roma, holding on to second overall after struggling in the sand dunes, was a little more than half an hour ahead of De Villiers, while Russian Leonid Novitskiy, in fourth, was 57 minutes behind the South African.
"I am happy to finish this special, once again a very difficult stage," De Villiers said.
"We had to stop several times to deflate the tyres.
"We saw Nani stuck in the sand, just like Robby [Gordon, fifth overall].
"We ended up leading the field - we did a good job.
"If we finish in this position tomorrow it will be like a victory for us."
The all-SA pairing of Duncan Vos and Robert Howie finished 15th in the stage, and were left chasing a top-10 position in the final leg after dropping one position to 11th overall in the cars category.
Debutant Mark Corbett and co-driver Francois Jordaan stormed across the line in 14th but also fell one place, to 24th, in the standings.
"It was a good stage for us, our best so far," Corbett said.
"We did very well in the sand dunes after starting in 17th place on the road and were up to 11th when we got stuck for the first time.
"Cars and trucks were marooned all over the place and we were lucky to only lose about 20 minutes altogether after twice having to dig ourselves out of the sand."
Of the 161 cars that started the two-week race in Mar de Plata, Argentina, only 79 remained ahead of the final stage.
The motorcycle contingent had been reduced from 178 to 98, while only 12 of the original 30 quads and 60 of the 74 trucks were still running.
"It's all catching up with us now, and Francois and I, and I'm sure our entire team, will be very relieved to see the finishing podium in Lima," Corbett said.
"Our aim was to finish and it looks like we're going to achieve this."
In the bikes division, South African Darryl Curtis, competing in the race for the first time, continued his late surge as he finished 24th in the penultimate stage, moving up one position to 22nd overall.
"Today's special was dangerous with big drop-offs and a lot of dunes," Curtis said.
"I crashed three times, but nothing serious other than a few bruises."
The only other SA rider left in the race, Greg Raaf, was 95th in the stage but held on to his overall position of 84th.
