The storm cut power for 50,000 people and caused the suspension of hundreds of flights. Most evacuation orders were lifted on Tueday as the storm pulled away from Japan's eastern coast.
At the height of the storm on Monday, authorities warned of an "imminent threat to life" and urged 1.9 million people to move to shelters. BBC reported.
The fatalities were from landslides in Kanagawa and Chiba prefectures. Six others were reported missing, public broadcaster NHK reported.
sustained winds of 130km/h (81mph) and gusts of 194km/h.
The typhoon is the latest in a series of storms in the Pacific, made more intense by the "super El Niño", which has warmed the ocean, fuelling the formation of storms.
Authorities had advised the public to pay attention to weather information.
Dujuan, which is Japan's 25th typhoon of the year, hit in the midst of a five-day holiday and forced the cancellation of several events.
Concerts scheduled for Monday at the Rock in Japan music festival were cancelled, while the Tokyo Game Show, a video game convention, also cancelled Monday's programme.
Japan's Prime Minister Sanae Takaichi offered her condolences in a post on X to those who lost their lives in the typhoon, before saying she would be continuing with her scheduled trip the United States as planned.
