The home side were allowed to cross at will at times and rack up their biggest score in an international match.
The victory handed Matt Williams his first victory as Scotland coach on home soil, although very little can have been learnt from such a one-sided contest.
Williams' men started as they meant to go on when Ally Hogg went over in the right corner in the second minute after Allan Jacobsen had burst clear from a maul on the halfway line.
The prop's perfect pass found Chris Cusiter, who sent flanker Hogg clear to canter in for his third try for Scotland.
But Japan hit back almost immediately when, after excellent recycling from the tourists, left-winger Hayato Daimon crossed on the fifth-minute mark.
Williams' men struck again on 20 minutes when Hugo Southwell was fed by Paterson to cross for his first of the evening, before Paterson added another himself soon after.
Scotland put together some more fluent phases of play before the break and their pressure wore down Japan sufficiently for Dan Parks to dummy his way over after 37 minutes.
The home side put the seal on an impressive end to the half when Jon Petrie picked up in loose play and galloped virtually unchallenged from just inside Japan territory followed by another from Paterson.
Next up to join the try-fest was Andy Henderson, who strolled over after Scotland stole the ball in a maul midway inside the Japan half and brought up his side's half-century before Paterson brought up his hat-trick after polishing off a great move.
Touchdowns from Graeme Morrison and Sean Lamont followed before flanker Donnie Macfadyen scrambled over on hands and knees for Scotland's 12th try ten minutes from time, and Russell and then Southwell also crossed as Japan became virtual spectators.
London Irish hooker Russell dived over in the dying seconds and Paterson knocked over his 11th conversion to bring up the century and cap an incredible result.
Scotland: Hugo Southwell; Chris Paterson, Ben Hinshelwood, Andrew Henderson, Sean Lamont; Dan Parks, Chris Cusiter; Allan Jacobsen, Gordon Bulloch, Gavin Kerr, Stuart Grimes, Nathan Hines, Allister Hogg, Jon Petrie, Donnie Macfadyen
Replacements: Robbie Russell, Craig Smith, Scott MacLeod, Jason White, Mike Blair, Gordon Ross, Graeme Morrison.
Japan: Ryohei Miki; Koichiro Kubota, Seiichi Shimomura, Yukio Motoki, Hayato Daimon; Keisuke Sawaki, Wataru Ikeda, Yuichi Hisadomi, Takashi Yamaoka, Ryo Yamamura, Takanori Kumagai, Hitoshi Ono, Naoya Okubo, Hajime Kiso, Takuro Miuchi.
Replacements: Mitsugu Yamamoto, Masahito Yamamoto, Feletliki Mau, Takatoyo Yamaguchi, Kiyonori Tanaka, Masatoshi Mukoyama, Hideyuki Yoshida