Powerful slammed into on Saturday, killing at least two people and prompting authorities to issue their highest level of disaster warning over "unprecedented" downpours that caused flooding and landslides.
Around 7.3 million people were placed under non-compulsory evacuation orders and more than 30 people were injured, four seriously.
Even before making landfall, Hagibis caused enormous disruption, forcing the cancellation of two Rugby World Cup matches, delaying the Japanese Grand Prix and grounding all flights in the Tokyo region.
It crashed into Japan's main Honshu island just before 19:00, barrelling into Izu, a peninsula southwest of Tokyo, the Japan Meteorological Agency (JMA) said, packing gusts of wind up to 216km/h (134 miles per hour) around an hour.
The storm claimed its first victim hours before arriving on the coast, when strong winds from its outer bands flipped a car in Chiba east of Tokyo and killed the driver.
But it was Hagibis' torrential rain that prompted the JMA to issue its highest-level emergency warning for parts of Tokyo and the surrounding areas, warning of disaster.
"Unprecedented heavy rain has been seen in cities, towns and villages for which the emergency warning was issued," JMA forecaster Yasushi Kajiwara told reporters.
"The possibility is extremely high that disasters such as landslides and floods have already occurred. It is important to take action that can help save your lives."
At least two landslides were already confirmed, with a man in his sixties killed in one in Gunma north of Tokyo.
By early evening, tens of thousands were in shelters and receiving emergency rations and blankets, though a 5.7-magnitude quake that rattled the Tokyo area did little to calm nerves.
Among the evacuees were people whose homes were damaged by a powerful typhoon that hit the region last month.
"I evacuated because my roof was ripped off by the other typhoon and rain came in. I'm so worried about my house," a 93-year-old man told national broadcaster NHK as he sheltered at a centre in Tateyama in Chiba east of Tokyo.
In Yokohama, outside of Tokyo, others hunkered down in their homes despite the storm.
"I'm 77 and I've never seen anything like this," Hidetsugu Nishimura told AFP.
"We can hear an infernal din from the rain and the wind, and a fragment of the roof has gone. For an hour, the house was shaking from wind and rain."
Even in the hours before the storm neared land, its outer bands brought tornado-like gusts of wind to Chiba, east of Tokyo, where one home was destroyed and several damaged.
Five people including a three-year-old boy were sent to hospital, but none suffered serious injuries, the local fire department told AFP.
Rugby, F1 disrupted
In Gotemba, west of Tokyo, the fire department said it had rescued one man who fell into a swollen canal but was still searching for a second man.
The JMA has forecast half a metre (20 inches) of rain for the Tokyo area in the 24 hours to midday on Sunday, with more for the central Tokai region, but many rivers were already close to breaching their banks by Saturday afternoon.
In Kanagawa, authorities implemented an emergency discharge as the Shiroyama dam reached capacity, with warnings issued for people living downstream.
Across the regions affected by the storm, more than 180 000 people lost power.
And everything from auto plants to the country's ubiquitous convenience stores, usually open 24 hours a day, shut their doors.
The storm has forced the delay of Japanese Grand Prix qualifiers scheduled for Saturday and the cancellation of two Rugby World Cup matches: England-France and New Zealand-Italy.
It could also jeopardise a key match-up between Scotland and Japan on Sunday. Officials are not expected to make a final decision on that game until Sunday morning, after they have assessed any damage to the venue and transport links.
Scotland face elimination if the match is axed and have warned they could take legal action if the game is cancelled. World Rugby called the threat "disappointing".
And organisers warned Saturday night that a Namibia-Canada fixture could be cancelled in Kamaishi, which was hit by the 2011 earthquake and tsunami disaster.
Japan is hit by around 20 typhoons a year, though the capital is not usually badly affected.
Hagibis is bearing down on the region just weeks after Typhoon Faxai hit the area with similar strength, killing two and causing major damage in Chiba.