Du Toit will combine in the second row with Ruan Nortje for the first of two tests between the teams after Etzebeth failed a fitness test on an injured knee.
Erasmus has made nine changes from the second Championship test against Australia two weeks ago. South Africa lead with two wins. New Zealand and Argentina have a win each. Australia lost both of their first two matches.
Du Toit's move to the second row also has been forced by injuries to locks R G Snyman, Franco Mostert, Jean Kleyn, Salmaan Moerat and Lood de Jager.
"Eben may have been ready to play this week if we really needed him," Erasmus said. "But we feel we will benefit more from selecting a player who is 100 per cent fit."
Salmaan likely will be "back in the selection frame next week," Erasmus added. "We're happy that things will ease significantly for us in that department going into the second test (at Cape Town)."
Among other changes to the team that beat Australia 33-12 in Perth, Jasper Wiese returns to the back row after a six-week suspension and Aphelele Fassi takes over from Willie le Roux at fullback.
The South Africa line-up includes 12 players who featured in last year's Rugby World Cup final against New Zealand which the Springboks won by a point.
"There is also no doubt (New Zealand) still will be hurting from the Rugby World Cup final and in addition to that they know how important a win will be to square things up and open up the Rugby Championship log," Erasmus said.
South Africa (v New Zealand): Fassi, Kolbe, Kriel, De Allende, Arendse, Feinberg-Mngomezulu, Reinach; Wiese, Dixon, Kolisi (capt), Nortje, du Toit, Malherbe, Mbonambi, Nche.Â
Reserves: Marx, Steenekamp, Koch, Van Staden, Louw, Smith, Williams, Pollard.
