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.
Saturday's reports came a day after floods struck in several areas of Jordan, including Petra, and the searches for missing people continue.
Flash floods caused by heavy rain across Jordan killed 11 people Friday and forced hundreds of tourists to seek higher ground in the kingdom's ancient city of Petra, government officials and official media said.
Civil defence divers searched for five people whose vehicle was swept away by floods in the Madaba area, southwest of the capital, state news agency Petra said.
Government spokeswoman Jumana Ghneimat said authorities had found alive four Israeli tourists who had gone missing in the Wadi Rum desert in southern Jordan but were looking for two more. The Jordanian military said that that it has sent soldiers and helicopters to assist in search operations.
"Rescuers are searching for five people who are missing in that area", the source said.
An excavator is partially submerged in a stream after rain storms unleashed flash floods, in Madaba city, near Amman, Jordan, November 10, 2018.
"One of the civilians was evacuated to the hospital for medical treatment while the three other civilians did not need any medical attention", the IDF statement said Saturday.
The deaths come more than two weeks after October 25 floods in the Dead Sea region of Jordan cost 21 lives, a lot of them children on a school trip.
It broadcast footage of tourists sheltering on high ground on both sides of the access road to Jordan's biggest attraction.
The bad weekend weather also saw over 3,700 tourists evacuated by the authorities from the world famous historic site of Petra.
She said more heavy rain was expected on Saturday and residents in affected areas were being urged to evacuate their homes.
Jordan's ministry of education also ordered schools closed across the country on Sunday.
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.