Jebi appears to have caused damage to the region's infrastructure on an unusual scale.
In the tourist magnet of Kyoto - home to ancient temples and shrines - it brought down part of the ceiling of the main railway station, while in nearby Osaka, the high winds peeled scaffolding from a multi-storey building.
Prime Minister Shinzo Abe, criticised for an initially slow response to devastating floods in July, posted repeated updates on the rescue efforts at Kansai.
"We continue to make utmost efforts to respond to disaster damage and restore infrastructure," he said.
Fallen trees at Kyoto's famous Arashiyama bamboo grove in the wake of #TyphoonJebi's landfall in Japan https://t.co/KxS6cG5o3m (Video: Yingyu Lee) pic.twitter.com/kP6CKY1TEi
— Channel NewsAsia (@ChannelNewsAsia) September 5, 2018
Businesses, factories and schools in the affected area shut down while the storm barrelled across the country, forcing the cancellation of hundreds of flights, ferry services and some bullet trains.
Economists said it was too early to gauge the storm's impact on local industry, with much depending on how long the airport remained closed.
Around 10 per cent of Japan's exports leave from Kansai airport, said Yusuke Ichikawa, senior economist at Mizuho Research Institute.
"Logistics could be affected as it may take time for Kansai airport to restart operations," he told AFP.
Debris seen at Kyoto Station a day after parts of its glass ceiling fell onto the atrium, narrowly missing commuters #TyphoonJebi https://t.co/KxS6cG5o3m (Video: Yingyu Lee) pic.twitter.com/m6HC3Qd3h0
— Channel NewsAsia (@ChannelNewsAsia) September 5, 2018
But with other airports and ports nearby, companies might be able to reroute shipments to minimise disruption, he added.
Japan's JXTG Nippon Oil & Energy Corp shut at least one of the refining units at its 135,000 barrels-per-day Sakai refinery in Osaka in western Japan due to typhoon damage to part of the cooling tower, the trade ministry said.
Many chip plants operate in the Kansai region. Toshiba Memory, the world's second-largest maker of flash memory chips, was monitoring developments closely and may need to ship products from other airports if Kansai remains closed, a spokeswoman said.
She said the company was not expecting a major impact because its plant in Yokkaichi in central Japan had not been affected by the typhoon.
Jebi's course brought it close to parts of western Japan hit by rains and flooding that killed more than 200 people in July but most of the damage this time appeared to be from the wind.
Despite its strength, the storm was far from the deadliest Japan has seen in recent years.
In 2011, Typhoon Talas killed at least 82 people in the area, while in 2013, a storm that hit south of Tokyo left 40 people dead.
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