The hosts were lethargic in the first half and led only 11-3 courtesy of a Seymour try and two Greg Laidlaw penalties.
Japan, nicknamed The Brave Blossoms, lived up to their billing and trailed by only one point after 55 minutes thanks to the lively Kenki Fukuoka who scored either side of Seymour's second try.
Any hope of an upset was snuffed out though with Scotland pulling away in the final quarter thanks to four further tries from Laidlaw, Alasdair Dickinson, Duncan Weir and Sean Lamont.
The Japanese recorded a famous 23-8 victory against a weakened Wales side in Tokyo in June but defeat means they are yet to register a win against a Six Nations side in Europe.
Scotland have now won four of their nine matches under temporary head coach Scott Johnson who led them to a third place finish in this year's Six Nations. Johnson will be replaced by the current head coach of French side Clermont Auvergne, Vern Cotter, in 2014.
Scotland host South Africa next weekend before the visit of Australia on Nov. 23.
