Tuivasa-Sheck will start at inside centre alongside Braydon Ennor, with Perofeta starting at fullback in Ian Foster's team.
Halfback Finlay Christie will play his second test in the number nine jersey, with incumbent Aaron Smith providing cover from the bench. Richie Mo'unga will direct traffic at flyhalf.
Despite some relatively new faces in the backline, Foster has named a strong forward pack, with Sam Cane back to lead the side.
Midfielder Anton Lienert-Brown returns on the bench after missing the start of the season with injury.
"This northern tour is going to be huge," Foster said in a statement.
"We see four incredibly tough tests ahead and this one against Japan will ask some serious questions of us.
"We want to show that we are ready to respond."
A number of first-choice players will miss the Japan test due to injury and personal reasons, including lock Sam Whitelock and the Barrett brothers.
New Zealand won back-to-back tests against Australia to successfully defend their Rugby Championship title in September.
After Japan, the All Blacks travel to Europe to face Wales, Scotland and England.
Team: 15-Stephen Perofeta, 14-Sevu Reece, 13-Braydon Ennor, 12-Roger Tuivasa-Sheck, 11-Caleb Clarke, 10-Richie Mo'unga, 9-Finlay Christie, 8-Hoskins Sotutu, 7-Sam Cane, 6-Shannon Frizell, 5-Tupou Vaa'i, 4-Brodie Retallick, 3-Nepo Laulala, 2-Dane Coles, 1-George Bower
Replacements: 16-Samisoni Taukei'aho, 17-Ofa Tu'ungafasi, 18-Tyrel Lomax, 19-Patrick Tuipulotu, 20-Dalton Papali’i, 21-Aaron Smith, 22-David Havili, 23-Anton Lienert-Brown
