The road connecting the two, which many pilgrims use to reach Mecca, was closed on Thursday once the rains began.
At least two people died on Thursday as heavy rains hit the western parts of Saudi Arabia including the coastal city of Jeddah.
According to officials, incoming flights have also been delayed as a result of the torrential weather and schools were also shut, Khaleej Times reports.
"Two deaths have been recorded so far, and we call on everyone not to go out unless necessary," the Mecca regional government said on its Twitter page.
The Mecca region includes Jeddah, the kingdom's second-largest city of roughly four million people, and Mecca city, the holiest city in Islam where millions perform the hajj and umrah pilgrimages each year.
The road connecting the two, which many pilgrims use to reach Mecca, was closed on Thursday once the rains began, state media reported, although it was later reopened, authorities said.
According to the Saudi Press Agency earlier, public, private and international schools in Jeddah, Rabigh, and Khulais would be shut on Thursday due to expected rainy conditions throughout the Makkah region.
The decision was made based on reports from Saudi Arabia's National Centre of Meteorology, which predicted heavy thunderstorms.
The Kingdom's two primary universities — King Abdulaziz University and the University of Jeddah — have followed suit. Final exams have been postponed for the first semester, with alternative dates expected to arrive later.
The Saudi Civil Defence has also issued a statement regarding the extreme weather conditions, saying that "light to heavy rain and strong winds were expected".
The authority has instructed residents to follow the necessary safety guidelines, as well as cautioning them to stay away from stagnant rainwater.
Incoming flights have also been delayed as a result of the torrential weather.
Jeddah Airport's official website shows a large number of arrivals on carriers such as Gulf Air, Turkish Airlines and Saudia set back by multiple hours – with one flight even delayed by 5. Others, such as a flight originally arriving into Jeddah, have been diverted entirely.
Earlier in the day, the King Abdulaziz International Airport took to Twitter to confirm the delay in the "departure of some flights". Passengers were further advised to "contact their airlines before heading to the airport to confirm their flight times".
Videos on social media showed cars being swept away by fast-moving currents, as muddy torrents poured through residential buildings and villas. Rows upon rows of cars can be seen in others, submerged and with windows broken.
Winter rainstorms and flooding occur almost every year in Jeddah. Floods killed 123 people in the city in 2009.