Babar and Rizwan were already dropped from the T20I series in New Zealand earlier this year, while Afridi did play against Black Caps he has also now been axed.
Salman Agha will lead the 16-man squad for whom there is a recall for Sahibzada Farhan, who is the leading run-scorer in the ongoing Pakistan Super League (PSL) with 394 runs at a strike rate of 154.50 playing for Islamabad United.
Also returning to the side are Hasan Ali and Saim Ayub with the latter missing since suffering s serious knee injury in the Test series in South Africa in January.
The Pakistan have selectors opted to include Fakhar Zaman, Hussain Talat Faheem Ashraf, Mohammad Wasim and Naseem Shah to give the squad more experience.
Pakistan's three-match series against Bangladesh is also going to be Mike Hesson's first assignment as white-ball head coach after he joined earlier this month.
The matches against Bangladesh will be played on May 28 and 30, and June 1.
Pakistan T20 squad: Salman Agha (capt), Shadab Khan (vice-capt), Abrar Ahmed, Faheem Ashraf, Fakhar Zaman, Haris Rauf, Hasan Ali, Hassan Nawaz, Hussain Talat, Khushdil Shah, Mohammad Haris (wk), Mohammad Wasim, Muhammad Irfan Khan, Naseem Shah, Sahibzada Farhan (wk), Saim Ayub
Pakistan's new Test bowling coach Ashley Noffke says the management are just looking 'add positivity' into the squad ahead of third and final Test against England that starts in Birmingham on Wednesday.
Former fast bowler Shoaib Akhtar reveals the Pakistan Cricket Board (PCB) has completely lost faith in the Test team and is looking to rebuild the squad with younger players.
Pakistan interim Test coach Mike Hesson admits the "last couple of days have been challenging" but says the players are used to "chaos" ahead of the third Test against England next week.
Pakistan Cricket Board director of high performance Aaqib Javed has called out batter Imam-ul-Haq, criticising the opener for not going out to bat in the second Test against England at Lord's.
