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The 20-year-old pacer suffered the injury during Pakistan's Super Four clash with arch-rivals India in the Asia Cup in Sri Lanka.
Fellow quick Haris Rauf is likely to recover ahead of the World Cup, which begins on October 5.
Pakistan's pace attack will be led by Shaheen Shah Afridi and he will be supported by Haris Rauf, Mohammed Waseem and Ali in a largely unchanged side led by Babar Azam.
The margin of victory - 228 - was the biggest by runs in an India-Pakistan ODI, bettering Pakistan's 180-run triumph in the 2017 Champions Trophy final.
The Pakistan team management said quicks Shahnawaz Dahani and Zaman Khan have been included as back-ups for Rauf and Naseem in their Asia Cup squad.
The pacer will be replaced by 22-year-old Zaman Khan, who has yet to make his ODI debut.
The 16-year-old Naseem Shah would eclipse former home captain Ian Craig as the youngest Test debutant on Australian soil.
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