More than 910,000 people were affected by cancellations and delays of almost 1,300 conventional train services and of 10 shinkansen bullet train services by JR East.
The storm caused widespread disruption, with many flights and trains cancelled.
Pedestrians protect themselves from wind and rain from typhoon Trami in Tokyo on Monday.More news: Elon Musk calls SEC the 'Shortseller Enrichment Commission' in tweet
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.
Over 400,000 households, mainly in eastern Japan, were still without power on Monday morning.
After Trami made landfall, one person was killed by a landslide in Tottori, western Japan, and another drowned in Yamanashi, west of Tokyo, public broadcaster NHK said.
Huge crowds built up at Tokyo train stations, people battling for spots in jam-packed commuter trains.More news: Wife of Malaysia's ex-PM Najib charged with money laundering
Kansai global airport in Osaka, the third busiest airport in Japan, suspended services on Sunday and resumed on Monday.
After pummelling Japan's outlying islands including Okinawa, Trami made landfall south of the city of Osaka on Sunday night.
Train services were also suspended in different parts of the country as well as in the outskirts of Tokyo but resumed on Monday.
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Deadly record rainfall hit western Japan earlier this year and the country sweltered through one of the hottest summers on record.