Typhoon Trami made landfall on Sunday at 20:00 local time (11:00 GMT) near the western city of Osaka, with gusts of up to 216 km/h (134 mph).
The storm caused widespread disruption, with many flights and trains cancelled. More than 750,000 homes lost power.
At least 120 people were injured. The typhoon comes less than a month after the country's strongest storm in 25 years hit western Japan.
Typhoon Jebi caused widespread flooding and at least seven deaths in early September.
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.
Two more people were reported missing and more than 120 were injured, officials were quoted as saying.
On Monday, commuters faced long delays as trains were delayed or cancelled because of trees blown on to tracks.
Kansai Airport, in Osaka, closed its runways when the storm swept in but reopened them on Monday. However, an estimated 200 flights were disrupted by the typhoon.
About 400,000 homes and offices were still without power on Monday.