The 19-year-old has been replaced in the squad to face Namibia and the T20 series against Pakistan by seamer Ottneil Baartman. Lizaad Williams is his replacement for the One Day Internationals on the subcontinent.
Maphaka was injured in a domestic four-day fixture last week and subsequent medical assessments indicated a Grade 1-2 injury which will require rehabilitation over the next four weeks.
South Africa play three T20s in Pakistan between October 28-November 1, and three ODIs from November 4-8.
South Africa squads for Pakistan tour:
T20I squad: David Miller (captain), Ottneil Baartman, Corbin Bosch, Dewald Brevis, Nandre Burger, Gerald Coetzee, Quinton de Kock, Donovan Ferreira, Reeza Hendricks, George Linde, Lungi Ngidi, Nqaba Peter, Lhuan-dre Pretorius, Andile Simelane, Lizaad Williams.
ODI squad: Matthew Breetzke (captain), Corbin Bosch, Dewald Brevis, Nandre Burger, Gerald Coetzee, Quinton de Kock, Tony de Zorzi, Donovan Ferreira, Bjorn Fortuin, George Linde, Kwena Maphaka, Lungi Ngidi, Nqaba Peter, Lhuan-dre Pretorius, Sinethemba Qeshile, Lizaad Williams.