The train operations were resumed gradually from Monday morning.
Huge crowds built up at Tokyo train stations, people battling for spots in jam-packed commuter trains.
A train on the Keio Line collided with a wall that had collapsed over a railway in the capital's Setagaya Ward around 4:45 a.m. The company said it was the first time it had stopped services early in Tokyo and surrounding areas after informing the public of its plans beforehand.
Train services were also suspended in different parts of the country as well as in the outskirts of Tokyo but resumed on Monday.
Major airports throughout airport including Tokyo's Narita and Haneda cancelled flights from to and from the city.
More than 120 people were injured in the powerful storm, public broadcaster NHK said.
Shinkansen trains between Shin-Osaka and Hiroshima were also suspended as were numerous local rail services.
Kansai Airport, in Osaka, closed its runways when the storm swept in but reopened them on Monday.
Japan has seen a spate of typhoons in recent months, including Jebi in early September and Shanshan and Jongdari in August, each causing bunkering delays at ports and barge congestion.
The typhoon, rated by Tropical Storm Risk as a category 1, the lowest on a five-point scale, killed two people and injured nearly 130, public broadcaster NHK said.
Airlines including Japan Airlines and All Nippon Airways canceled many flights Monday as well because massive cancellations of flights the previous day made it hard for them to arrange aircraft.