The typhoon first made landfall in the southern part of Tokushima Prefecture at 12 pm (local time), before striking for the second time near Kobe city at around 2 pm (local time), The Japan Times reported.
Packing winds of up to 216km/h, Jebi is currently hovering near Anan city in Tokushima Prefecture.
Both Nippon Airways and Japan Airlines have announced the cancellation of nearly 600 flights.
In the wake of extreme conditions, the weather agency has asked people to remain vigilant on chances of flooding and mudslides due to the typhoon.
Evacuation orders have been issued in some parts of Osaka, Kyoto, Nara, Hyogo, Kagawa, Ehime and Wakayama prefectures.
There were also reports of blackouts in Gifu, Aichi and Mie prefectures.
As the typhoon struck Tokushima Prefecture, a 67-year-old man sustained injuries while trying to cover the roof of his house with a sheet, amid the violent and gusty winds.
Another man in his 60s fell two metres into a rice paddy field in Mima city, the report said.
The Meteorological Agency further said that Typhoon Jebi is expected to cross over the Sea of Japan by late Tuesday, drifting further north, and would weaken to an extratropical cyclone by Wednesday morning.
While around 500 mm of rainfall is likely to pound central Japan, another 400mm of downpour might fall in the western part of the country.
The after-effects of the storm are unlikely to be felt in Tokyo.
Japanese Prime Minister Shinzo Abe, who has been campaigning across the country ahead of the ruling Liberal Democratic Party’s leadership election later this month, cancelled his trip to Kyushu region to take stock of the situation.
Japan has been hammered by typhoons in the past and other disasters related to heavy downpour, including massive flooding and landslides that claimed over 220 lives in July.