Government spokeswoman Jumana Ghneimat said the highway was cut in both directions.
Twelve people died in heavy rains and flooding in parts of Jordan on Friday and authorities evacuated foreign tourists from the ancient city of Petra and other popular destinations, officials said on Saturday.
At least nine people, including a young girl, were killed as flash floods engulfed multiple cities in Jordan on Friday, a government official said.
Authorities said Friday search was ongoing for several missing persons in Madaba governorate.
For his part, the Director of the Civil Defense of Ma'an Governorate, Salem Al Sarayrah, said that the weather conditions in Ma'an and Petra Governorates are very normal after the rains have stopped, pointing out that any emergency caused by rain storms is being dealt with.
To the east, three people were killed near Dabaa on the Desert Highway, one of Jordan's three main north-south arteries, while one was killed near Maan in the south.
In Petra, the ancient trade hub carved into rose-hued rocks, heavy rains began at around 1 p.m. Friday and last for about 40 minutes, said Rafael Dorado, 41, a tourist from Spain.
The latest deaths come after October 25 flash floods in the Dead Sea region of the kingdom killed 21 people, majority children on a school trip.
In Wadi Musa, the town next to Petra in southern Jordan, water surged from nearby mountains into a dry riverbed running through the community.
Authorities declared a state of emergency in the Red Sea port city of Aqaba further south as downpours started in the afternoon.
It broadcast footage of tourists sheltering on high ground on both sides of the access road to Jordan's biggest attraction. There was a public outcry last month after 18 children on a school trip were swept away, leading to the resignation of the country's education and tourism ministers.
Thousands of persons were rescued from various disaster areas, including hundreds of tourists in Petra, she said.
Jordan's ministry of education also ordered schools closed across the country on Sunday.