Officials warned of flooding in coastal areas as the storm brought maximum sustained winds of 123 miles per hour.
It caused a massive blackout in Shizuoka Prefecture, where there were power cuts in more than 700,000 homes.
Two people were reported missing, and more than 120 people were injured in the powerful storm, public broadcaster NHK said.
A powerful typhoon brought down trees onto railway tracks and kicked up debris across Tokyo as it brushed past the Japanese capital early on Monday, killing two people and stranding thousands as train lines were closed or severely delayed.
"I won't make it on time because trains are way behind schedule", said a woman in her 40s who was commuting to her office in Fuchu, western Tokyo.
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After making landfall near the city of Tanabe in the western prefecture of Wakayama in Honshu around 8 pm Sunday, the typhoon swept through the main island also including the Kanto eastern region and the Tohoku northeastern region.
At its height, Trami packed gusts of 216 kilometres (134 miles) per hour, though it weakened as it moved over land.
Central Japan Railway Co., meanwhile, suspended all Shinkansen bullet trains services on the Tokaido Shinkansen Line between Tokyo and Shin-Osaka after 5:00 p.m. (0800 GMT) Sunday.
Trami is the latest in a string of extreme weather and natural disasters to hit Japan, which has suffered typhoons, flooding, earthquakes and heatwaves in recent months, claiming scores of lives and causing extensive damage.
Deadly record rainfall hit western Japan earlier this year and the country sweltered through one of the hottest summers on record.