Spain's former world rally champion Carlos Sainz overcame poor visibility to take the overall lead in a congested Dakar Rally on Sunday after winning the second stage, a 237km special from Santa Rosa to Puerto Madryn.

The Volkswagen driver finished ahead of the Mitsubishi of France's Stephane Peterhansel, the defending champion, by 1min 14sec, and 1:56 in front of his South African teammate Giniel De Villiers.

Saturday's opening stage winner Nasser Al-Attiyah of Qatar, in a BMW, finished ninth, 6min 32sec behind Sainz.

"It was a very difficult stage with all the dust and the bikes," admitted Sainz who won the Rally of Argentina twice during his world rally championship career.

"At times, we nearly had to stop. I even hit a biker at one point; I hope he?s going to be OK."

Peterhansel, who is bidding for a 10th Dakar title after winning the motorcycle section six times and the car event on three occasions, was satisfied with his second place after a disappointing sixth spot in Saturday's opener from Buenos Aires.

"This special stage was a bit more technical. There was some off-terrain work for the first time, so we had to be on our guard," he explained.

"I caught up with (Mitsubishi teammate) Luc (Alphand) at one point. After that, we ended up in the dust thrown up by the bikers.

"There were some sections with quite thick vegetation. We were almost stopped at that point, because visibility was down to one or two metres. The bikers were all over the place, so we had to be very careful."

Sainz will go into the third stage on Monday with an overall lead of 2min 19sec over De Villiers while Peterhansel is 3:51 off the pace.

Japan's Hiroshi Masuoka, the 2002 and 2003 champion, pulled out overnight after experiencing engine problems with his Mitsubishi. The 49-year-old eventually finished the opening stage, almost five hours off the lead.

De Villiers too admitted visibility had been a problem on Sunday.

"The start of the special was very quick, but as soon as we arrived in the off-track part, it was not very easy to navigate and we got a little bit lost. We must have lost a minute or two," he said.

"Then in the last section, there was lots of fesh-fesh (very soft sand), so it was very difficult to get past the bikers."

Dutch rider Frans Verhoeven won the motorbike stage.

The KTM rider finished ahead of France's former champion Cyril Despres (KTM) by 40 seconds while another Frenchman David Fretigne riding a Yamaha was third, 1min 04sec adrift.

"In the middle, there was a very difficult navigation section in amongst the vegetation and with the dust, it was impossible to see any tyre tracks," said Verhoeven who had been fourth overnight.

"I managed to find the route and at one time I saw there were no more tyre tracks in front of me, so I knew I was in the lead."

Spanish rider Marc Coma retained the overall lead despite finishing around 12 minutes behind Verhoeven.