As the typhoon made landfall, a 71-year-old man was found dead under a collapsed warehouse, likely due to a strong wind, and a man in his 70s fell from the roof of a house and died, NHK public television reported, adding more than 90 were injured.
A hulking tanker ship smashed right into a bridge linking Osaka Kansai airport with the Japanese mainland.
Prime Minister Shinzo Abe urged Japanese citizens "to take action to protect your lives, including preparing and evacuating early", while Japan's weather agency has issued warnings for landslides, flooding and high tides as well as lightning and tornadoes across western Japan, including in major cities Osaka and Kyoto, Agence France-Presse reports.
High waves hit breakwaters at a port of Aki, Kochi prefecture, Japan, on Tuesday.
A composite image showing the air conditions in Japan with Typhoon Jebi and a large oil tanker that has been pushed into a bridge.
Typhoon Jebi, packing winds of up to 216 kilometres per hour, made landfall around midday in western Japan near areas still recovering from deadly record rains earlier this summer. At least one person has been killed and several others injured as Jebi brought violent winds to the west of the country.
Wind gusts of up to 166 km/h were recorded in one part of Shikoku, with forecasts for gusts as high as 216km/h.
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He said: "When we joined up on the 15th June we made it clear that it was the first thing we could achieve together as a squad and as a team".
Based on its wind speeds, Jebi was classified as "very strong" by Japan's weather agency.
Other video showed roofs being torn off houses, transformers on electric poles exploding and a auto scudding on its side across a parking lot.
More than 700 flights were cancelled, including several global flights departing and arriving at Nagoya and Osaka, along with ferries, local train services and some bullet train lines.
The severe weather has left tens of thousands without power and forced the cancellation of hundreds of flights as well as trains and ferries.
In Osaka, the Universal Studios Japan theme park and US Consulate were both closed.
More than 1.6 million households were without power in Osaka, Kyoto, and four nearby prefectures.
Toyota Motor Corp. said it will suspend its nighttime operations at 14 plants across the nation, including in Aichi, Fukuoka and Miyagi prefectures.
Toyko has remained largely unscathed from the storm but will face high winds and heavy rain.