Mafi missed Japan's opener against Russia due to injury and comes into the run-on side as a replacement for Kazuki Himeno.
Brave Blossoms head coach Jamie Joseph has sprung a surprise by starting his captain Michael Leitch on the replacements bench which means Pieter Labuschagne will lead the side.
Elsewhere, prop Koo Ji-won, second-row Luke Thompson and full-back Ryohei Yamanaka make their first start after coming off the bench in their victory against Russia.
Himeno moves from number eight to the blindside flank, where he takes over from Leitch, and William Tupou switches from full-back to wing.
Prop Asaeli Ai Valu, lock Wimpie van der Walt and wing Lomano Lemeki all drop to the bench alongside Leitch, while flanker Hendrik Tui has been left out.
Wing Kenki Fukuoka, who hurt his right calf in a warm-up game against South Africa on September 6 is also an absentee.
Japan: 15 Ryohei Yamanaka, 14 Kotaro Matsushima, 13 Timothy Lafaele, 12 Ryoto Nakamura, 11 William Tupou, 10 Yu Tamura, 9 Yutaka Nagare, 8 Amanaki Lelei Mafi, 7 Pieter Labuschagne (c), 6 Kazuki Himeno, 5 James Moore, 4 Luke Thompson, 3 Jiwon Koo, 2 Shota Horie, 1 Keita Inagaki
Replacements: 16 Atsushi Sakate, 17 Isileli Nakajima, 18 Asaeli Ai Valu, 19 Wimpie van der Walt, 20 Michael Leitch, 21 Fumiaki Tanaka, 22 Rikiya Matsuda, 23 Lomano Lava Lemeki
Date: Saturday, September 28
Venue: Shizuoka Stadium Ecopa
Kick-off: 16:15 local (08:15 BST, 07:15 GMT)
Referee: Angus Gardner (Australia)
Assistant Referees: Jérôme Garcès (France), Matthew Carley (England)
TMO: Ben Skeen (New Zealand)