Wilson will make his first Scotland start, replacing
the injured Kelly Brown
, with Greig Laidlaw taking over the leadership duties.
A further three changes are made on the bench involving Jon Welsh, Alastair Kellock and David Denton.
Johnson said: "I'm hard pressed to remember so many injuries from the one Test match, but it's a fact and we just have to get on with it.
"I'd said from before we left Scotland that we wanted to find out about players through this tour and, perhaps, because of circumstances, some of that is being accelerated.
"But there's no doubt for me that our three new caps, for example, have had strong seasons for Glasgow and have worked really diligently on the training fields out here to earn their chance.
"We've faced South Africa a fair bit in the last decade and right now they're the second best team in the world, playing on their own paddock and with a win against Italy already under their belts.
"We have to be competitive and, once again, I'll reiterate that we have to get our accuracy and aggression 100% at breakdown to give ourselves the opportunity."
: W Le Roux; B Habana, JJ Engelbrecht, J De Villiers (capt), B Basson; M Steyn, R Pienaar; T Mtawarira, A Strauss, J Du Plessis, E Estebeth, J Kruger, M Coetzee, A Botha, P Spies.
: B Du Plessis, T Nyakane, C Oosthuizen, F van der Merwe, S Kolisi, P van Zyl, P Lambie, J Serfontein.
: Peter Murchie, Tommy Seymour, Alex Dunbar, Matt Scott, Sean Lamont, Ruaridh Jackson, Greig Laidlaw (capt), Alasdair Dickinson, Scott Lawson, Euan Murray, Tim Swinson, Jim Hamilton, Alasdair Strokosch, Ryan Wilson, Johnnie Beattie.
: Stevie Lawrie, Jon Welsh, Moray Low, Alastair Kellock, David Denton, Henry Pyrgos, Peter Horne, Duncan Taylor.
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