Henry was the only uncapped player selected in the 34-man squad for matches against the Brave Blossoms in Osaka on Aug. 8 and Townsville a week later.
However, Queensland lock Lukhan Salakaia-Loto and New South Wales Waratahs prop Isaac Kailea have returned after missing out on Joe Schmidt's final Wallabies squad for the Nations Championship tests against Ireland, France and Italy.
Kailea replaces Australia's most capped player James Slipper in the squad, having earned the last of his eight Wallabies caps in 2024 in his debut test season.
The Wallabies will be without several established players, including starting centre Len Ikitau, who is sidelined by a minor ankle injury, while powerhouse loose forward Tom Hooper continues to recover from a shoulder problem.
Veteran scrumhalf Jake Gordon and young flyhalf Tom Lynagh are also unavailable, but Reds number 10 Carter Gordon, who suffered a calf strain in the 33-31 loss to Ireland, has been retained.
Number eight Harry Wilson will continue to captain the squad under Kiss.
"Selection is always a challenging process, but as coaches we've looked to bring together a group based on form, cohesion and how we want to play the game," Kiss said in a statement.
"Spending time with the group over the last few weeks alongside (assistant coaches) Scott McLeod and Jonny Fisher has been incredibly valuable as we look to hit the ground running."
Wallabies squad to face Japan:
Forwards: Allan Alaalatoa, Miles Amatosero, Angus Bell, Charlie Cale, Josh Canham, Isaac Kailea, Fraser McReight, Josh Nasser, Zane Nonggorr, Brandon Paenga-Amosa, Billy Pollard, Aidan Ross, Lukhan Salakaia-Loto, Lachlan Shaw, Carlo Tizzano, Taniela Tupou, Rob Valetini, Jeremy Williams, Harry Wilson (capt).
Backs: Jock Campbell, Filipo Daugunu, Ben Donaldson, Carter Gordon, Isaac Henry, Max Jorgensen, Ryan Lonergan, Tate McDermott, Declan Meredith, Hunter Paisami, Dylan Pietsch, Harry Potter, Joseph-Aukuso Suaalii, Kalani Thomas, Tom Wright.