The PCB expects the 28-year old opener to be out for "three to five" weeks, making his participation in the Boxing Day Test in Centurion unlikely.
Fakhar reportedly complained about pain in his right knee after engineering a run-out during the second T20I against Australia in October.
Despite the pain, Fakhar played five limited-overs games with the injury before deciding to take time off to heal the injury. Hence he is not in the squad for the ongoing Tests against New Zealand.
He will meet the PCB's medical team at the National Cricket Academy in Lahore on Tuesday to chalk up a plan for his recovery.
The selectors have already begun the process of shortlisting players for the South Africa tour. The Test squad will most likely be similar to the one currently taking on New Zealand.
Fakhar made his Test debut in October and is now a key member of the side. However, the injury situation means another player is likely to get a chance at the top of the order.
Pakistan will play three Tests, five ODIs and three T20Is during their tour to South Africa.
First Published: December 1, 2018, 1:31 AM IST