Brisbane Heat confirmed the decision followed consultations with PCB medical staff. Afridi sustained the injury while bowling against the Adelaide Strikers, where he was seen limping off and pointing to his right knee.
He later said on social media that he had been called back for rehab, thanking the Heat and their fans for their support and expressing hope of returning to action soon.
Afridi played just four matches for the Heat, taking two wickets at an economy rate of 11.19. His season included a difficult debut outing in which he was removed from the attack for dangerous bowling after delivering two waist-high full tosses.
Despite limited on-field impact, his stint marked his first experience in the BBL, alongside fellow Pakistan internationals Babar Azam, Mohammad Rizwan and Haris Rauf.
Heat CEO Terry Svenson praised Afridi's professionalism and influence on younger bowlers, sentiments echoed by acting captain Xavier Bartlett, who highlighted the value of his advice within the squad.
The PCB's cautious approach is shaped by Afridi's history of right knee issues, including a serious injury in 2022 that affected his previous World Cup campaign.
With the next global tournament only weeks away, Pakistan have opted to prioritise his recovery. Brisbane Heat are now exploring replacement options for the remainder of the BBL season.