It was the first time the Scots had played in front of home fans since November 2019 and a crowd of 2,346 were at the DAM Health Stadium to watch an exciting Test match.
Rhona Lloyd scored two tries and was named played of the match, with Lana Skeldon, Megan Gaffney, Chloe Rollie and Lisa Thomson also touching down.
The Scots trailed 12-10 at the break, even though Japan had a player sent off in the 20th minute.
Malcolm said: “We weren’t happy at half-time because, although we showed glimpses of what we could do, we weren’t good enough.
“After the break we were more clinical, our attack sharpened up and defensively we were strong.
“This keeps the momentum up we built up with two wins in September.”