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The SA Rugby Union said in a statement on Friday that Muller had failed a late fitness test on his hamstring injury ahead of the Boks' second Pool D match in Wellington, New Zealand.
Springbok coach Peter de Villiers said team management had planned for such an eventuality and Willem Alberts would act as lock cover among the replacements.
"It’s not an ideal situation, but that’s tournament rugby," De Villiers said.
"We knew this was a possibility from earlier in the week so we have made our plans.
"It's a long tournament and we have to be sensible and there was no point risking making Johann's injury worse."
Veteran lock Victor Matfield had already been omitted from the team while recovering from a hamstring injury, and Bakkies Botha was selected in the run-on XV despite the Bok medical team stating earlier in the week that he was not responding well to treatment for his Achilles injury.
Teams:
South Africa: 15 Pat Lambie, 14 Odwa Ndungane, 13 Jaque Fourie, 12 Frans Steyn, 11 JP Pietersen, 10 Morne Steyn, 9 Fourie Du Preez, 8 Pierre Spies, 7 Schalk Burger, 6 Heinrich Brussow, 5 Danie Rossouw 4 Bakkies Botha, 3 Jannie Du Plessis, 2 John Smit (captain), 1 Gurthro Steenkamp
Substitutes: 16 Bismarck du Plessis 17 Tendai Mtawarira 18 Francois Louw 19 Willem Alberts 20 Fancois Hougaard 21 Ruan Pienaar 22 Juan de Jongh
Fiji: 15 Kini Murimurivalu, 14 Vereniki Goneva, 13 Gaby Lovobalavu, 12 Seremaia Bai, 11 Naipolioni Nalaga, 10 Waisea Sedre Luveniyali, 9 Nemia Kenatale, 8 Sakiusa Matadigo, 7 Akapusi Qera, 6 Dominiko Maiwiriwiri Waqaniburotu, 5 Wame Lewaravu, 4 Leone Nakarawa, 3 Deacon Manu (captain), 2 Sunia Koto, 1 Campese Ma'afu
Substitutes: 16 Telemaitoga Dautu Tuapati, 17 Waisea Nailago, 18 Netani Edward Talei, 19 Sisa Koyamaibole, 20 Vitori Tomu Buatava, 21 Nicky Little, 22 Gaby Lovobalavu
