Winger Taira Main has been elevated from the bench in last month's loss to France to an otherwise unchanged backline.
Jack Cornelson has switched from No. 8 to the second row to make way for the returning Faulua Makisi.
Jones has rotated his props again, bringing Takato Okabe and Shuhei Takeuchi in to shore up the front row.
Openside flanker Kanji Shimokawa is the other change in the pack, with Ben Gunter moving to the blindside.
Japan have never beaten Australia in seven previous matches.
Japan team to face Australia:
Starters: 15-Takuro Matsunaga, 14-Kazuma Ueda, 13-Dylan Riley, 12-Samisoni Tua, 11-Taira Main, 10-Ryunosuke Ito, 9-Naoto Saito, 8-Faulua Makisi, 7-Kanji Shimokawa, 6-Ben Gunter, 5-Warner Dearns (captain), 4-Jack Cornelson, 3-Shuhei Takeuchi, 2-Hayate Era, 1-Takato Okabe
Replacements: 16-Mamoru Harada, 17-Sojiro Otsuka, 18-Keijiro Tamefusa, 19-Harry Hockings, 20-Michael Leitch, 21-Tiennan Costley, 22-Shunsuke Uenobo, 23-Yoshitaka Yazaki
Australia team:
Starters: 15-Tom Wright, 14-Max Jorgensen, 13-Joseph Suaalii, 12-Hunter Paisami, 11-Harry Potter, 10-Declan Meredith, 9-Ryan Lonergan, 8-Harry Wilson (captain), 7-Fraser McReight, 6-Rob Valetini, 5-Miles Amatosero, 4-Josh Canham, 3-Allan Alaalatoa, 2-Josh Nasser, 1-Aidan Ross.
Replacements: 16-Billy Pollard, 17-Angus Bell, 18-Taniela Tupou, 19-Jeremy Williams, 20-Charlie Cale, 21-Tate McDermott, 22-Ben Donaldson, 23-Isaac Henry