The climax to the group stage at Yokohama's International Stadium had been in serious doubt as a magnitude 5.7 quake coincided with Hagibis hitting Japan's east coast.
The storm left at least two dozen people dead and scores more injured but the game went ahead and Japan secured a thrilling 28-21 victory to set up a last-eight tie with South Africa.
Wales will face France in the quarter-finals after ending their Pool D campaign with an unconvincing 35-13 victory over Uruguay, while Tonga beat the United States 31-19 and the Pool B clash between Namibia and Canada in Kamaishi was cancelled.
Here, the PA news agency wraps up Sunday's Rugby World Cup action.
Be careful what you wish for
Scotland withstood both a typhoon and an earthquake on the eve of their win-or-bust showdown with Japan but found themselves blown out of the World Cup as the super-charged hosts claimed victory in Yokohama.
Finn Russell put Scotland ahead early on but the Brave Blossoms hit back with a series of ceaseless attacks to secure top spot in Pool A and a rematch with their 2015 victims South Africa in Tokyo next Sunday.
Kenki Fukuoka grabbed a double, while star winger Kotaro Matsushima crossed over for his fifth of the tournament, but it was prop Keita Inagaki who finished off a stunning move that will be hard to beat for try of the tournament.
Scotland refused to go down without a fight but second-half scores from forwards WP Nel and Zander Fagerson were not enough to prevent the Scots suffering their second pool exit in three tournaments.
Wales set up showdown with France
Wales secured a World Cup quarter-final clash against France after ending their Pool D campaign with an unconvincing victory over Uruguay.
The Six Nations champions only led by a point at half-time following prop Nicky Smith's try that full-back Leigh Halfpenny converted.
Josh Adams then claimed his fifth touchdown of the tournament, with Halfpenny again adding the extras, but Uruguay stayed in touch through two Felipe Berchesi penalties.
A 65th-minute penalty try took Wales further ahead and – although Berchesi converted hooker German Kessler's touchdown – Warren Gatland's side added further scores in the final seven minutes from Tomos Williams and Gareth Davies.
Tonga come out on top
Tonga came from behind at half-time to secure victory over the United States and avoid finishing bottom of Pool C.
Tonga opened the scoring through a Siegfried Fisi'ihoi try after 16 minutes, but the USA rallied with two tries in the space of five minutes from Mike Teo.
Tonga took the lead after 61 minutes when Telusa Veainu chipped over the top, chased his own kick and hacked the ball on for Viliami Lolohea, who fed Hingano to score.
Just four minutes later ,Tonga extended their advantage with their third try from captain Siale Piutau and – although Tony Lamborn burrowed over from close range – Tonga secured the bonus point with their fourth try right on the whistle when Veainu latched onto James Faiva's kick and touched down.