Amir, who has been an automatic selection for Pakistan in all three formats of the game since his return to international cricket, had hurt his right shin during the second Test in Abu Dubai.
The left-arm pacer has been advised two to three weeks rest after he underwent an MRI scan following complaints of pain in his right shin.
However, he has been picked in the T20 squad after rehab in the hope that he will recover in time. Sarfraz Ahmed will lead the side.
Meanwhile, veteran all-rounder Mohammad Hafeez, who had been omitted from the squad that played the three-match T20 series against the World XI, has been included in the 16-member squad.
Umar Amin, Faheem Ashraf and Aamer Yamin, among the players brought in for the World XI series, retain their spots.
The first two matches will be played in Abu Dhabi on October 26 and 27 before teams fly to Lahore for the final game on October 29.
Squad: Sarfraz Ahmed (captain), Fakhar Zaman, Ahmed Shahzad, Babar Azam, Shoaib Malik, Mohammad Hafeez, Imad Wasim, Shadab Khan, Mohammad Nawaz, Faheem Ashraf, Hasan Ali, Amir Yamin, Mohammad Amir (subject to fitness clearance), Rumman Raees, Usman Shinwari, Umar Amin (ANI)