Eddie Jones had always feared his side would struggle to back up their magnificent win over South Africa given their incredibly short four-day turnaround for this encounter.
The Australian was proved right as they out of steam during the final 30 minutes, but until that point they had given another exemplary display of commitment and talent to show the victory over the Boks was no fluke.
They led early on through Amanaki Mafi’s try and trailed by just two points shortly after the interval, but that proved to be the moment Scotland assumed control.
Flanker John Hardie, centre Mark Bennett (two), wing Tommy Seymour and fly-half Finn Russell all crossed for second-half tries, with man-of-the-match Greig Laidlaw kicking 20 points on the ground where he plays his club rugby.
It leaves Vern Cotter’s men top of what is now a wide open pool ahead of their clash with the USA in Leeds on Sunday.
But Japan once again emerged with huge credit and coach Jones, to his credit, refused to use his side’s ridiculously short preparation time as a reason for their defeat.
“We are a fit side and we kept running. We just weren’t good enough,” said Jones.
“We are not going to use the turnaround as an excuse, they scored 33 points in the second half to our three. But we needed to be better.
“Ideally you need a six-day turnaround but you have to suck it up and do your best and they were better than us.”
Gloucester scrum-half Laidlaw kicked two early penalties for Scotland, but were given a shock when Japan took the lead from their first real attacking platform.
Grant Gilchrist conceded a needless penalty and, when the Brave Blossoms opted for the touchline they set-up a maul that allowed Mafi to dot down, with Ayumu Goromaru converting.
However, ill-discipline allowed Scotland to quickly regain the lead through another brace of Laidlaw penalties and Japan were soon a man down when wing Kotaro Matsushima was binned for an illegal steal.
However, Japan managed to get through the 10 minutes without conceding any further points, and when Goromaru buried Seymour into touch as Scotland threatened on half-time another upset looked possible.
The momentum appeared to be with the Japanese when Mafi went on a rampaging run upfield and Goromaru kicked a penalty to put them within two points of the Scots.
But, when Mafi was stretchered off with a serious injury the game changed, and a break from Sean Lamont was soon making the ground for flanker Hardie to finish in the corner.
It was Scotland’s first World Cup try for 290 minutes and, having ended the long wait, a few more followed quickly.
Stuart Hogg’s slashing break sent in Mark Bennett for the first of the centre’s brace, before Seymour picked off a loose pass in midfield to race 70 yards and out the result beyond doubt.
There was still time for Bennett to battle through some weak tackling to wrap up the bonus point and Russell finished things off after a concerted attack. “I would not say it was a convincing win. We scored points in the second half after trading blows in the first half,” said Cotter.
“But we have a bonus point which we are very happy with and hats off to Japan. They are a good side who bring an attacking threat, but we are happy to get started as it has been nervy watching everyone else play.
“The boys kept their composure and came away with the win.”
Hogg (Maitland 66); Seymour, Bennett (Horne 72), Scott, Lamont; Russell, Laidlaw; Dickinson (Grant 65), Ford (Brown 71), Nel (Welsh 71), Gilchrist (R Gray 50), J Gray, Wilson (Strauss 58), Hardie, Denton.
Tries – Hardie, Bennett (2), Seymour, Russell. Conversions – Laidlaw 4. Penalties – Laidlaw 4. Japan: Goromaru; Matsushima, Sa’u, Tamura, Fukuoka; Tatekawa (Hesketh 73), Tanaka (Hiwasa 64); Inagaki (Mikami 41), Horie (Kizu 72), Yamashita (Hatekeyama 53), Thompson (Ito 65), Ives (Makabe 61), Leitch, Broadhurst, Mafi (Tui 45).
Try – Mafi. Conversion – Goromaru. Penalty – Goromaru.
John Lacey (IRFU)