Kolbe scored twice against Italy but picked up an injury and was kept out of the Springboks' final Pool B match against Canada as a precaution to ensure he was ready for the quarters.
Coach Rassie Erasmus had rotated his squad through the pool stage to ensure his players all had game time before the knockout stage but has settled on the same matchday squad that played against Italy, with a 6-2 split between forwards and backs in the replacements.
"A lot of guys put up their hands and played really well and we wanted to get some continuity into the team," Erasmus told a media conference on Thursday.
"There were a few difficult selections but we felt given what we achieved against Italy and in the interests of combinations and continuity this was the best team to pick."
Erasmus said the 6-2 split on the bench was not an indication they would try to simply dominate the smaller Japanese forwards.
"The way Japan play is that they do exploit your tired and bigger forward defenders late in the first and second half so we think with our selection, two fresh forwards might nullify that space they want to use," Erasmus said.
He added that the selection of Bongi Mbonambi as the starting hooker with Malcom Marx coming off the bench was due to the pace that they expected Japan to play.
Mbonambi was better suited for a tighter role while Marx would be better "when the game opened up", Erasmus said.
Captain Siya Kolisi will start his third match in succession, and play his fifth game at the tournament, after he returned from an injury-ravaged season in the Springboks' tournament opener against the All Blacks.
"We will probably try and play the game at our pace and they will try and play at theirs," Erasmus said.
"It will be a great tactical battle.
"There are a lot of expectations in a quarter-final and it's who handles the pressure the best."
Team: 15-Willie le Roux, 14-Cheslin Kolbe, 13-Lukhanyo Am, 12-Damian de Allende, 11-Makazole Mapimpi, 10-Handre Pollard, 9-Faf de Klerk, 8-Duane Vermeulen, 7-Pieter Steph du Toit, 6-Siya Kolisi (captain), 5-Loedwyk De Jager, 4-Eben Etzebeth, 3-Frans Malherbe, 2-Bongi Mbonambi, 1-Tendai Mtawarira.
Replacements: 16-Malcom Marx, 17-Steven Kitshoff, 18-Vincent Koch, 19-RG Snyman, 20-Franco Mostert, 21-Francois Louw, 22-Herschel Jantjies, 23-Frans Steyn.