The Scots rarely looked convincing in Toyota City but did enough to take a 26-13 win in the first game of the two Test series.
Scotland's points came from a try by WP Nel and the boot of Greig Laidlaw. Scotland were also awarded a first-half penalty try.
Scotland head coach Vern Cotter said: "First of all, I'm happy - the win is what we were after.
"The way we got it was probably done in a complicated fashion. We gave the ball back to them a number of times and had to work our defence. We did work our defence and I thought we defended reasonably well.
"Our set piece held up without being great but it was still holding up and gave us a platform."
Cotter may call up a replacement for Alasdair Dickinson after the prop came off injured early in the first-half.
"We'll have to have a look at Al Dickinson," said Cotter.
"Bit of a concern and we'll be looking at alternatives. If he can't take the field next week, we'll look at bringing somebody over."
Cotter is hopeful other knocks picked up at the Toyota Stadium can be managed before next Saturday's match in Tokyo.
"Huw Jones should be okay [to provide cover in the backs]," said the New Zealander. "Hopefully we'll be able to fill the absence of Duncan Taylor [at centre] if he can't play with what we've got.
"WP Nel was a little bit sore coming off, also. [We'll have] a full assessment, see if these guys can be back at 100% and we may have to rotate the team a bit."