World Rugby issued a statement saying an evacuation order remained in place in the Kamaishi area where the game was set to be played on Sunday, and there had been landslides and flooding in the vicinity of the stadium.
"Following extensive discussions with World Rugby, Kamaishi City and Iwate Prefecture, during which we considered every possibility to make this game happen, in the end we had no option but to cancel the match to ensure the safety of the fans, team, volunteers, and all others involved," organising committee chief executive Akira Shimazu said.
"It was both a difficult and emotional decision to make, however I feel it's the right decision and firmly believe both domestic and foreign fans will understand the decision was made to ensure safety."
Two of Saturday's three scheduled games were cancelled well before the destructive typhoon made landfall.
Organisers will assess conditions in Yokohama before making a decision on Japan's last Pool A game against Scotland later on Sunday. There is a feeling the match could go ahead, possibly behind closed doors.
A cancellation would see the match declared a draw and Scotland, who need to win, would be eliminated from the World Cup.
"The safety of all involved in Rugby World Cup 2019 is our primary consideration and fans are advised not to travel to Kamaishi or the venue, which will be closed," World Rugby said.
The New Zealand vs. Italy at Toyota and England vs. France at Yokohama were the first games ever to be cancelled at rugby's showpiece event.
Cancelled matches are logged as 0-0 draws, and teams get two competition points each. Canada and Namibia were both winless in the group stage, so the cancellation had no impact on the quarter-finals.
The Japan Meteorological Agency had forecast the typhoon to be the worst to hit Japan in six decades. It brought heavy rainfall in wide areas of Japan all day ahead of its landfall early Saturday evening, and continued to batter parts of the main island with heavy winds and torrents of rain overnight.
An earthquake with a preliminary magnitude of 5.7 shook the areas drenched by the rainfall, shortly before the typhoon made landfall in Shizuoka prefecture.