Marco Jansen, Keshav Maharaj, Kagiso Rabada and Tristan Stubbs will also sit out the T20 series because of their involvement in the Tests, but will play in the three One-Day Internationals between the two countries later in the month.
Oft injured fast bowler Anrich Nortje and spinner Tabraiz Shamsi return to the T20 side for the first time since the T20 World Cup in June, where South Africa reached the final.
Allrounder George Linde has also been named in the squad for the first time in three years.
The first match is in Durban on December 10, followed by back-to-back clashes in Pretoria on December 13 and in Johannesburg the following day.
South Africa and Pakistan then meet in three ODIs on December 17, December 19 and December 22 before beginning a two-Test series on December 26.
South Africa T20 squad:
Heinrich Klaasen (capt), Ottneil Baartman, Matthew Breetzke, Donovan Ferreira, Reeza Hendricks, Patrick Kruger, George Linde, Kwena Maphaka, David Miller, Anrich Nortje, Nqaba Peter, Ryan Rickelton, Tabraiz Shamsi, Andile Simelane, Rassie van der Dussen.
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