As the storm approached, Japanese Prime Minister Shinzo Abe called a disaster response meeting and cancelled a trip to Kyushu, the country's southernmost main island.
Of the 11 deaths, eight people died in the western prefecture of Osaka, including four men, who fell from upstairs or the roofs of their houses after apparently being hit by strong winds, broadcaster NHK reported.
"More than anything else, I really want to take a bath", one woman told NHK public television.
About 3,000 tourists were stuck overnight at Kansai Airport in western Japan, an important hub for companies exporting semiconductors built on reclaimed land on a bay near Osaka and connected to the mainland by a bridge that was damaged when a tanker slammed into it during the storm.
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Each of the boats that crashed had a mix of family and friends from out of the area, some of whom were rescued by passing boaters. Two helicopters searched by air, and divers were sent out into the river's waters, which can range from shallow to 30 feet deep.
Airport officials said Wednesday it may remain closed for around a week.
In central Osaka, the wind sent a 100-metre-tall ferris wheel into a furious spin, even though its power had been cut off.
Cranes damaged by Typhoon Jebi are seen in Nishinomiya, western Japan.
Boats were ferrying stranded passengers from Kansai International Airport one of the country's busiest - after thousands of people were forced to spend the night in the partially flooded facility.
Local media said more than a million households were left without power by the storm, and evacuation advisories were issued for almost 1.2 million people, though only another 16,000 were under stronger - though still not mandatory - evacuation orders.
"I urge the Japanese people to take action to protect your lives, including preparing and evacuating early", he said.
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The typhoon may also bring further downpours to areas that were devastated by sudden rainfall in early July that killed more than 200 people.
Kansai airport is critical for business as well, exporting 5.6 trillion yen ($50 billion) worth of goods, mostly computer chips, electronics parts and other machinery, primarily to Asian destinations, such as China and South Korea, but also to the USA and Europe, according to Osaka Customs.
More than half a million households in and around Osaka remained without power this morning. In just 48 hours, the storm morphed from a tropical storm into a bonafide Category 5 monster with sustained winds up to 175 mph.
Japan usually suffers the attacks of typhoons in summer, but this year has been particularly hard.
At least six people have died and 160 people have been injured since the typhoon made landfall Tuesday afternoon, September 4, bringing strong winds and lashing rain, according to Japanese public broadcaster NHK.
The flooding and landslides proved so deadly in part because many people did not heed evacuation advisories, which are not mandatory.
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