The typhoon moved away from Japan’s coast and out into the Pacific by morning, allowing authorities to lift or downgrade most heavy rain and landslide warnings.
Dujuan had already led to the early closure in the capital of the one of the world’s biggest video game trade fairs.
Japan often sees strong typhoons in the late summer and early autumn, with other storms this season disrupting some events at the Asian Games being held in the country.
The Fire and Disaster Management Agency said one person died in Kanagawa prefecture, near Tokyo, while a local official told AFP that another died in Chiba.
Search operations were continuing for four people missing after landslides triggered by torrential rain, according to public broadcaster NHK said.
More than 46,000 households in Chibam near Tokyo, were still without electricity on Tuesday morning.
Although Dujuan weakened as it moved northeast, it dumped record rainfall in parts of the Tokyo area.
Oshima, an island about 120 kilometers south of central Tokyo, recorded 832 millimeters of rain over 48 hours, more than double its average rainfall for the whole of September, NHK reported.
Rainfall in Tokyo’s Edogawa Ward reached a record 282.5 millimeters over 24 hours.
Scientists say human-driven climate change is intensifying the risk posed by heavy rains because a warmer atmosphere holds more water.