On Monday landslides and flooding prompted evacuation orders for nearly two million people.
By Tuesday morning, Japan's Fire and Disaster Management Agency had recorded one death in Kanagawa Prefecture, southwest of Tokyo, and another in Chiba, east of the capital.
It also reported one person seriously injured and five with minor injuries, as well as damage to at least 56 homes.
Kanagawa authorities, meanwhile, reported four people missing following several landslides.
Dujuan brought record rainfall to Oshima, on the island of the same name.
The Japan Meteorological Agency recorded 832mm of rain in the 48 hours leading up to midnight on Monday, the highest accumulated total for that period in Oshima since records began in 1991.
The landslide alert for Oshima was raised to the highest Level 5 on Monday, though it was downgraded to Level 4 later.
At the height of the storm, the Fire and Disaster Management Agency placed 1.9 million people across six prefectures under evacuation orders, including more than 1.1 million residents of Kanagawa.
The air traffic tracking platform Flightradar24 reported on Facebook the previous day that the storm along Japan's east coast had caused the cancellation of nearly 500 flights at Haneda and Narita airports.
Dujuan also forced the early closure of the Tokyo Game Show, Asia's largest video game trade fair held in Chiba. The event concluded on Sunday instead of Monday.
On Tuesday morning the typhoon was located east of Japan and moving away to the northeast at 50km/h, with sustained winds of 126km/h and gusts of up to 180km/h.
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