"While the evacuation order was lifted, we urged residents to be cautious as we expect heavy rains tonight," said Naoyuki Kato, a police official in the hardest-hit city of Okazaki, 90km southwest of Tokyo.
About 100 soldiers were dispatched to Okazaki to rescue hundreds of people stranded in their homes.
Some areas were left without power or telephone services after the storms and several rivers overflowed, forcing drivers to abandon their cars in the streets.
Rescuers paddled through flooded streets and canals in Okazaki in inflatable rafts on Friday, ferrying residents, many of them elderly, from destroyed homes to safety.
At the storm's peak, Okazaki was hit with 5.7 inches of rain per hour according to Japan's meteorological agency, a record for the area.
A 76-year-old woman was found drowned in her home in Okazaki and a man was in serious condition, Kazumi Yamagawa, a local police official said. Three other people were reported to be missing.
Hachioji, a western suburb of Tokyo, was also hit by record rainfall, triggering landslides that destroyed several homes.
Several train lines were affected and hundreds of people on their way to work in the city suffered delays.
Japan is often hit in summer by heavy rains, which can trigger flash flooding.
Earlier this month, five workers were killed in Tokyo after being pulled down a manhole when sewage waters suddenly rose after a thunderstorm.
Last month, a woman, two girls and a boy were found dead after being washed away by a swollen river after a downpour in the port city of Kobe, west of Tokyo.