Typhoon Melor, packing gusts of up to 162 kilometres an hour, cut a swathe across densely populated central Japan, causing travel chaos and power blackouts for hundreds of thousands of homes.
The typhoon, the first to make landfall in Japan since 2007, was "very dangerous", but weakened as it churned across the main island of Honshu, said Takeo Tanaka, a forecaster at the Meteorological Agency.
"Winds are violent and rain is torrential. You should also be on guard against mudslides," he said.
A 54-year-old newspaper deliveryman died in western Wakayama prefecture after his motorbike collided with a fallen tree, while a 69-year-old man was killed by a falling branch north of Tokyo, police said.
About 100 injured
About 100 people were injured and thousands more evacuated to shelters, the government said.
"It felt like a huge earthquake," one woman in Chiba prefecture east of Tokyo told local television.
"Before we knew it, the water level came up to our knees inside our house," said another resident in central Aichi prefecture.
There was severe travel disruption with nearly 500 flights cancelled and many railway services -- including bullet trains -- temporarily suspended.
Television footage showed trucks blown over and cars abandoned in the middle of flooded roads.
The economy also took a hit as manufacturers including Toyota Motor, the world's biggest automaker, halted production while the storm passed.
As many as 570,000 households in west and central Japan experienced power cuts, while blackouts hit about 16,000 homes and businesses in and around Tokyo.
The storm moved to the northern Tohoku region in the afternoon, leaving at least 31,000 households there without electricity, before heading back out into the Pacific Ocean.
Farmers rushed to harvest fruit before the typhoon arrived, while elsewhere dozens of cows escaped after their barn was damaged.
An Asian Cup qualifier between Japan and Hong Kong went ahead as planned after the city of Shizuoka avoided a direct hit from the typhoon, the Japan Football Association said.
The typhoon made landfall in central Aichi prefecture shortly after 5:00 am (2000 GMT Wednesday) and ripped across the main island on a path north of Tokyo, where blue skies had returned by Thursday afternoon.
The weather agency said heavy rain was expected to lash Hokkaido, the northernmost main island, through Friday although the storm was likely to be downgraded to a tropical depression on Saturday.
Typhoon not as devastating as feared
The typhoon, while fierce, did not appear to have been as devastating as some had feared. On Wednesday forecasters had described it as one of the worst storms to threaten the country in the past decade.
Japan has built extensive defences against floods and landslides, including storm surge barriers in coastal areas.
But typhoons can still be deadly. In October 2004 Typhoon Tokage killed 95 people in the archipelago.
Melor, which means jasmine in Malay, is the latest in a series of powerful typhoons to batter Asia in recent weeks.
In August, 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 Southeast Asia, killing hundreds of people, mostly in the Philippines and Vietnam. In Taiwan more than 600 people died after Typhoon Morakot struck in August.