It was not immediately clear when the stage would be completed, as Sunday was scheduled to be a rest day.
The stage between Salta and Tucuman was shortened because of flash flooding and the trucks' stage was cancelled.
While the motorbikes got through with mainly only navigational troubles, by the time the cars set off two hours later, dry riverbeds had turned into torrents.
The race was stopped at 88 kilometers, where a river couldn't be crossed, stranding Nasser Al-Attiyah, who was second overall in his buggy, and 2009 champion Giniel de Villiers in his Toyota.
Fifty cars had already passed that point but not all of them could finish. Guerlain Chicherit was the fastest to finish and overall leader Stephane Peterhansel was fifth home, but race officials may yet decide to scrub the entire stage. Peterhansel started the day three minutes ahead of Al-Attiyah.
"Everything was going smoothly for us. We were putting the pedal on the metal, and everything was fine," Al-Attiyah said. "When we got to the Rio (river), there were three meters of water. There was no way we could cross that. So we called the organizers, who told us the stage had been neutralized."
In motorbikes, Joan Barreda Bort of Spain won the 150-kilometer stage, his third stage win of the race, though he's out of title contention.
Casteu was nine minutes ahead of fellow Frenchman Cyril Despres, the defending champ, and 11:16 in front of Portuguese Ruben Faria. Pain finished 37 minutes back and slipped to fifth, 16:10 behind.
Despres faces a 15-minute penalty for swapping engines on his KTM overnight.
Casteu was one of the few who had a good day.
"A huge navigational success," he said. "I'm over the moon because it's difficult to ride at the front while attacking and keeping your bearings, navigating. I was able to keep my cool while everyone else was spinning around, but I stayed focused and was the first across the line. Leading the Dakar during the rest day, that's terrific."