Afridi, 25, suffered a knee cartilage injury while fielding during Saturday's win over Adelaide Strikers, Brisbane Heat said in a statement.
"After consulting with the Pakistan Cricket Board’s medical staff during the past 24 hours, it was agreed that Afridi would... return home for further treatment," it added.
Afridi, making his debut in the Australian franchise-based T20 league, took two wickets in four appearances for Heat.
"The BBL was everything I had heard it would be - lots of good, skilful cricket. I have enjoyed the challenge," Afridi said in a statement shared by the team.
Pakistan will begin their T20 World Cup campaign on February 7th with a group stage game against the Netherlands in Colombo.