Philander's injury combined with the one to Lungi Ngidi, who will be out of action until February due to knee issues, mean that Dale Steyn, Kagiso Rabada and Duanne Olivier will form the pace attack for the first Test.
"Duanne Olivier was the initial back-up bowler, so he will play, and Paterson will provide backup," Cricket South Africa selection convener Linda Zondi said.
"As far as Philander is concerned, his fitness will continue to be monitored for the second and third Tests."
Paterson, meanwhile, will have to wait for his Test cap. He has played three ODIs and eight T20Is and has 321 first-class wickets at 23.56.
"We have been looking at him for some time," Zondi said of Paterson. "He is a bowler who has performed on the domestic scene consistently for a long time and he will be our back-up for the first Test."
Faf du Plessis (capt), Hashim Amla, Temba Bavuma , Theunis de Bruyn, Quinton de Kock (wk), Dean Elgar, Zubayr Hamza, Keshav Maharaj, Aiden Markram, Duanne Olivier, Dane Paterson, Kagiso Rabada, Dale Steyn