Torrential rain led to the early part of the planned stage, which had been set for 492km, being cancelled.
But then violent storms returned and only a few cars made it to the finish after the race was stopped at the 88km mark when a river bed on the course swelled with water.
Guerlain Chicherit reached the finish in the fastest time with overall leader Stephane Peterhansel over 12 minutes behind.
Nasser al-Attiyah, who started the day second, was quickest when the race was stopped and almost three minutes ahead of Peterhansel but was among those who got stuck and watched several of his rivals disappear into the distance.
Al-Attiyah said: "There were three metres of water!"
"Everything was going smoothly for us, we were putting the pedal on the metal, and everything was fine. When we got to the río, there were three metres of water, there was no way we could cross that. So we called the organisers, who told us the stage had been neutralised at CP2."
He was left sweating on his fate as the stewards conferred and have yet to decide which times will be taken into account.