The tears began before kick-off. They fell during and just after a Japanese anthem haunting in its beauty and emotion. They continued during this most incredible of Rugby World Cup matches and they would have fallen for a long time afterwards as the Brave Blossoms sent them homeward to think again, as the opposition anthem famously says.

This match between Japan and Scotland marks the end of the pool phase and start of the knockout matches and it feels like the World Cup has properly begun. Japan are in a quarter-final for the first time by virtue of finishing Pool A in first place. Their reward is a mouthwatering clash against South Africa. Ireland, whom Japan famously beat in Shizuoka a couple of weeks ago, will face the All Blacks in theirs on Saturday.

That's another delicious prospect on several levels, but it can wait, as can the rest of the quarter-finals, because this effort by Kiwi coach Jamie Joseph, his countryman Michael Leitch and the rest of Japan's squad to get to this point deserves to be celebrated to the fullest.

Had this match been called off due to Typhoon Hagibis, Scotland would have gone home burning with righteous anger and begun the process of lawyering up. Now they're just going home, but they played their part – did they what.

Their threats to sue World Rugby should the organising body call off this fixture at Yokohama Stadium would have sounded not just hollow but faintly ridiculous had they not launched their second-half comeback which took this already electric match to a new level.

They were near buried at 28-7 two minutes after the break. That they came back to not just make a game of it but seriously worry the Japanese owed much to their mental fortitude and ability to handle the pace.

The Scots have built a reputation over the past couple of years of playing with style and freedom and giving the ball a bit of air. In the first half they were made to look positively pedestrian by the men in red and white jerseys who are taking the high-tempo game to another level in their homeland but once their two big men WP Nel and Zander Fagerson crashed over to narrow the gap to 28-21 after 55 minutes it was game on.

In the end they were beaten by Japan's almost superhuman energy and probably the best scrambling defence of this tournament. Fullback Stuart Hogg and first-five Finn Russell, in particular, can take a bow.

Japan needed only two points to qualify but they had their four-try bonus point two minutes into the second half when little left wing Kenki Fukuoka stripped the ball from a Scotland player, caught it, and ran in under the posts. He had scored his first of the night a minute before the break.

The crowd, who chanted "Nippon" throughout, couldn't believe what was happening. And to think this match could have been played before an empty stadium due to the deluge and high winds the day before.

There was a lot more of that sort of thing; loosehead prop Keita Inagaki catching a dipping ball after a brilliant interchange to go in under the posts – right wing Kotaro Matsushima, who scored a hat-trick in the opening game of the tournament against Russia way back on September 20 and the bonus point try in the 84th minute against Samoa, darted this way and that.

Shota Horie, the hooker with the crazy hair, was everywhere. Replacement loosehead prop Isileli Nakajima was a monster with bleach blond hair. No 8 Kazuki Himeno was all power, skipper Leitch a calm and steady presence with an uncanny ability to appear on the right touchline and steamroll a poor outside back.

For their mentor Joseph, a 49-year-old who played 29 tests for the All Blacks, this will represent his most significant achievement as a coach.

His team's commitment was absolute, but also, crucially, accurate. It also meant something hugely significant. Tighthead prop Jiwon Koo went off injured just after the first quarter, and was clearly upset. Every one of his teammates on the reserves bench went over and comforted him.

After weeks of caution and near cluelessness from some teams here, Japan are the all-action team this nation and tournament deserves. And don't count them out against the Boks next Sunday at Tokyo Stadium.

Japan 28 (Kenki Fukuoka 2, Kotaro Matsushima, Keita Inagaki tries; Yu Tamura 4 conversions)
Scotland 21 (Finn Russell, WP Nel, Zander Fagerson tries; Greig Laidlaw 2 conversions, Finn Russell conversion)
HT: 21-7