Afridi led Pakistan in the World Twenty20 held in India in March-April this year but stopped short of announcing retirement after the team exited in the group stages.
He featured in the Twenty20 tournament in England for Hampshire county but failed to give a performance of any note which forced the selectors to leave him out this time.
Opener Ahmed Shahzad and middle-order batsman Umar Akmal -- part of the team in the World Twenty20 -- were also not selected.
Chief selector Inzamam-ul-Haq said Afridi will be selected in the future if he performs better in domestic matches.
"I said this before that since there is only one match we will not consider Afridi, but once he gives a performance at a domestic level he will be given a chance," Inzamam told AFP.
"If Ahmed and Umar improve their discipline and performances they will also be considered for selection but since we have only one match on this tour we have tried to build the team for the future," said Inzamam.
Another opener Mohammad Hafeez was also not selected after he returned home mid-way in the ongoing one-day series against England suffering from a knee injury.
There was a recall for left-arm paceman Sohail Tanveer who last played a Twenty20 against England in November last year.
The 21-year-old all-rounder Amad Butt is the only uncapped player in the side.
Pakistan were playing the fourth one-day against England in Leeds on Thursday, having lost the first three matches.
They also drew a four-match Test series 2-2 last month on this same tour.
Pakistan's Squad: Sarfraz Ahmed (captain), Khalid Latif, Sharjeel Khan, Shoaib Malik, Mohammad Rizwan, Babar Azam, Mohammad Nawaz, Imad Wasim, Mohammad Amir, Wahab Riaz, Mohammad Irfan, Sohail Tanveer, Amad Butt