Japan lost 35-32 to the Wallabies in Osaka and Jones has shuffled his pack for Saturday's game in Townsville.
Waseda University's Yoshitaka Yazaki comes in on the right wing, with fellow student Ryunosuke Ito keeping his place at fly-half after an impressive performance against the Wallabies.
Shunsuke Uenobo starts at inside centre to win his third cap while Haruto Kida makes his fourth appearance on the left wing.
Jones made five changes to the starting line-up, with Tiennan Costley also coming in to play in the back row, and Harry Hockings returning at lock.
Japan team to face Australia:
Starters: 15-Takuro Matsunaga; 14-Yoshitaka Yazaki, 13-Dylan Riley, 12-Shunsuke Uenobo, 11-Haruto Kida; 10-Ryunosuke Ito, 9-Naoto Saito; 8-Faulua Makisi, 7-Tiennan Costley, 6-Ben Gunter; 5-Warner Dearns (capt), 4-Harry Hockings; 3-Shuhei Takeuchi, 2-Hayate Era, 1-Takato Okabe
Replacements: 16-Mamoru Harada, 17-Sojiro Otsuka, 18-Izi Sword, 19-Jack Cornelsen, 20-Michael Leitch, 21-Itsuki Kamimura, 22-Samisoni Tua, 23-Kazuma Ueda