Macleod has not featured for the Welsh national team since the autumn series in 2022 and will make up a back three that also includes Alex Mann and experienced number eight Taulupe Faletau.
Ben Carter and Teddy Williams are the second row pairing while hooker Dewi Lake, who captains the side, will have props Nicky Smith and Keiron Assiratti either side of him.
Flyhalf Sam Costelow starts after missing the Six Nations through injury, with Kieran Hardy at scrumhalf.
Ben Thomas and Johnny Williams make up the centre pairing, and there is a back three of wings Josh Adams and Tom Rogers, and full-back Blair Murray.
Replacement hooker Liam Belcher is the only uncapped player in the match day 23.
"We had a very good build-up. We tried to give everyone a fair chance of selection," stand-in coach Matt Sherratt said.
"(Macleod) has struggled with some injuries, had a real rollercoaster over the last three or four years, so him coming back in is massive.
"I think you could tell from the players’ reaction when Liam Belcher was selected how much he deserves it.
"He’s been in the regional game for ten years. He’s gone back to university to do an electrician’s degree and then he’s managed to work his way into the national squad."
Wales have not always got the reward their performances deserved in their horror 17-game losing run, and Sherratt is hoping they can keep their intensity throughout.
"I think an 80-minute performance, that physical edge and making sure that we transfer training into the game is going to be the biggest thing for us.
"It’s going to be humid. It’s going to be hot. Japan traditionally play quite a fast brand of rugby, so us getting up to speed with that is going to be key."
Wales team vs Japan:
15. Blair Murray, 14. Tom Rogers, 13. Johnny Williams, 12. Ben Thomas, 11. Josh Adams, 10. Sam Costelow, 9. Kieran Hardy
8. Taulupe Faletau 7. Josh Macleod, 6. Alex Mann, 5. Teddy Williams, 4. Ben Carter, 3. Keiron Assiratti, 2. Dewi Lake (captain), 1. Nicky Smith
(Replacements: 16. Liam Belcher, 17. Gareth Thomas, 18. Archie Griffin, 19. James Ratti, 20. Aaron Wainwright, 21. Tommy Reffell, 22. Rhodri Williams, 23. Joe Roberts)