Transport disruption was also widespread, with authorities halting suburban trains in Tokyo throughout most of Saturday, suspending several bullet train lines and cancelling all flights in and out of the capital's two main airports.
The other confirmed death was a man in his 60s killed in a landslide north of Tokyo.
They were among 80 people to sustain injuries in the typhoon, with nine still unaccounted for, according to national broadcaster NHK.
"Unprecedented heavy rain has been seen in cities, towns and villages for which the emergency warning was issued," JMA forecaster Yasushi Kajiwara told reporters.
"I evacuated because my roof was ripped off by the other typhoon and rain came in. I'm so worried about my house," a 93-year-old man told NHK as he sheltered at a centre in Tateyama in Chiba, east of Tokyo.
"We can hear an infernal din from the rain and the wind, and a fragment of the roof has gone. For an hour, the house was shaking from wind and rain."
Among the missing were three people swept away in their car after a bridge over the River Chikuma broke, local official Masataka Tomi told AFP.
Nearly half a million households in the greater Tokyo area lost power at some stage during the storm.
Organizers warned people not to travel to the northern town of Kamaishi, an area devastated by the 2011 tsunami where a match between Namibia and Canada was due to take place.Read more: ABS-CBN News
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Japan braces for powerful typhoon Hagibis
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