Dozens of vehicles were seen submerged in several areas.
It lashed the city with unprecedented strength resulting in destructive winds and floods with 115 miles per hour wind speed making Mekunu the strongest storm to ever hit the country.
Oman's directorate general of meteorology said the cyclone had gone inland and was heading northwest into Saudi Arabia, but that heavy rains would likely continue into Sunday.
Thousands of residents near coastal areas in Dhofar and al-Wusta had been moved to shelters as 170km/h (105mph) winds and torrential rain hammered the region, officials said.
Civil defence authorities said they had set up 65 shelter centres in the two affected provinces.
Strong winds had already generated 12-metre-high (40-foot-high) waves.
Omani transportation officials said the port of Salalah will remain closed but that the airport will open on Sunday, three days after it closed on Thursday.
Socotra's governor Ramzy Mahrous said five Yemenis had died on the island apart from the two Indians.
The search is ongoing for eight Indian sailors who went missing when the cyclone hit Socotra's port.
Four of the missing were crew on board a boat that sunk when the storm accompanied by strong winds and heavy rain hit the island in the Arabian Sea, Fisheries Resources Minister Fahad Kafin told AFP.
Around 1,000 families on Socotra, with a population of around 60,000, were evacuated after their homes were damaged.
The island, listed by UNESCO as a World Heritage Site, has been the focus of a dispute between the UAE and Yemen's internationally recognized government amid that country's war after Shiite rebels, known as Houthis, seized the Yemeni capital, Sanaa.
Saudi troops were deployed to Socotra earlier this month following tensions over an Emirati military presence on the island.
The labor ministry declared a three-day holiday for companies and establishments in the private sector, state news agency ONA reported.