Fakhar has struggled for consistency throughout the Asia Cup with a top score of just 27 and a total of 61 runs at an average of 20.33.
While Fakhar has failed to post any big scores during the Asia Cup, he did manage to contribute three consecutive ODI centuries against New Zealand at the start of the year and is ranked inside the top 10 in the ODI Batter Rankings, an ICC report said.
The left-hander has been replaced by youngster Mohammad Haris, in what is one of five changes Pakistan have confirmed for their crucial Super Four match against Sri Lanka in Colombo.
A trio of injuries forced Pakistan's hand at selection, with Naseem Shah, Haris Rauf and Salman Ali Agha (eye) all missing out, while all-rounder Faheem Ashraf has been omitted alongside Fakhar.
Fellow all-rounder Mohammad Nawaz is the direct replacement for Ashraf, while Mohammad Wasim and Zaman Khan get their chances to show their capabilities next to pace spearhead Shaheen Afridi in the absence of Naseem and Rauf.
Babar Azam's side need to defeat Sri Lanka to book a place at this year's Asia Cup decider against India, while Sri Lanka only need to avoid defeat to advance.
Pakistan: Mohammad Haris, Imam-ul-Haq, Babar Azam (c), Mohammad Rizwan (wk), Saud Shakeel, Iftikhar Ahmed, Shadab Khan, Mohammad Nawaz, Shaheen Afridi, Mohammad Wasim, Zaman Khan. (UNI)
