A 69-year-old man was killed in Saitama Prefecture, north of Tokyo, by a large branch that was ripped from a tree by the strong winds.
In Wakayama Prefecture in western Japan a newspaper deliveryman died when his motorcycle hit a fallen tree.
Dozens more people were injured, many by wind-blown debris or broken glass.
More than 300 flights were cancelled because of the storm, as were bullet train services.
In Tokyo overland train lines were temporarily suspended, stranding commuters in the busy morning rush hour.
A number of factories halted production in central Japan but managers said they would make up the lost output later.
Tens of thousands of households were without electricity in western Mie and central Gifu prefectures, while a blackout also hit 3,500 households in Tokyo and in neighbouring Kanagawa, power companies said.
Despite Japan's extensive defences against floods and landslides, including storm surge barriers in coastal areas, western Japan was battered in October 2004 by Typhoon Tokage, which killed 95 people.
In August this year, Typhoon Etau brought flash floods and landslides that killed at least 25 people in Japan, even though it avoided a direct hit.
Another powerful storm, Ketsana, has caused devastation across South East Asia, killing hundreds of people, mostly in the Philippines and Vietnam.
In Taiwan more than 600 people died after Typhoon Morakot struck in August.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.