Typhoon Phanfone has killed at least one person, a US airman on Okinawa who was washed away by high waves.
Thousands of households have lost power and Japan's two largest airlines have suspended many flights.
The storm also forced the suspension of the search for people missing after last week's volcanic eruption.
The storm-tracking website Tropical Storm Risk forecasts that Phanfone will rapidly lose power over the next few hours as it goes further into the Pacific Ocean.
Typhoon Phanfone was downgraded from an earlier status of a super typhoon, but the Japan Meteorological Agency had warned it was still a dangerous storm.
Japan averages 11 typhoons a year, according to its weather agency.
The typhoon made landfall on Monday morning near the central city of Hamamatsu, with winds of up to 180 km/h (112 mph).
The airman was one of three US military personnel swept away by high waves whipped up by the typhoon off southern Okinawa island, where the US has a large military base. The remaining two are still missing.
A police spokesman said they had been taking photographs of the sea.
A university student who was surfing off the seas of Kanagawa Prefecture, south of Tokyo, was also missing, national broadcast NHK reports. It said at least 10 people had been injured and 9,500 houses were without power.
The storm was expected to deposit about 100mm of rain on Tokyo over 24 hours, according to the Transport Ministry website.
Many schools were closed on Monday and two car companies in Japan halted production at some plants ahead of the storm.
More than 174 domestic flights were affected nationwide, NHK state broadcaster said on Sunday.
On Sunday, heavy rain delayed the Japanese Formula One Grand Prix in Suzaka. French driver Jules Bianchi lost control in the wet conditions and crashed, sustaining a severe head injury.
A powerful typhoon has brought many parts of Japan to a standstill and briefly battered Tokyo before heading out to sea.