Shizuoka city, southwest of the capital, Tokyo, was hit especially hard, seeing a record 417 mm (16.42 inches) of precipitation since the rain started on Thursday, the Japan Meteorological Agency (JMA) said.
Winds at the centre of Typhoon Talas were blowing at about 65 kph (40 mph), with peak gusts of about 90 kph (56 mph), it said.
A man in his 40s was killed in a landslide and a 29-year-old man was found dead after his car plunged into a reservoir, Kyodo reported.
Power was also cut to about 120,000 households, supplier Chubu Electric Power Grid Co said, adding that a landslide had knocked over two electricity pylons.
"We apologise deeply for the inconvenience caused by this power outage. The outage is being prolonged due to landslides, among other factors, but we are doing all we can to fix it as swiftly as possible," the company said on Twitter.
By Saturday afternoon, power had returned to the majority of households, though some 2,800 were still without power. Chubu Electric Power Grid estimated that it would take a few months for the pylons to be restored, according to Kyodo.
Central JR restarted some of its bullet train services, which had been suspended from Friday evening because of the rain.
Although the JMA downgraded the typhoon to an extratropical cyclone on Saturday morning, it forecast further torrential rain in Shizuoka and urged caution for landslides and flooding.
Yokohama city, some 30 km south of Tokyo, also issued an evacuation advisory at about noon on Saturday to about 3,000 residents.
typhoon nanmadol, one of the biggest storms to hit Japan in years, killed at least two people and brought ferocious winds and record rainfall to the west of the country on Monday.