Junaid, 21, picked up an abdominal problem which ruled him out of the fifth and final One-Day International against Sri Lanka in Abu Dhabi and misses the tour, which comprises a Twenty20 International, two Tests and three ODIs.
29-year-old Khalil has taken 122 first-class wickets since the start of the 2010/11 domestic season although he last played for Pakistan in 2005.
He went wicketless in a Test apiece against Australia (in 2004) and India (in 2005) while he took five wickets in three One-Day Internationals against Australia and the West Indies during Pakistan's tour of Australia in the 2004/5 season.
Junaid is expected to be out of action for around six weeks, which puts him in doubt for the series with England which begins in January.
Abdul Razzaq is also an injury doubt for the series, which begins on 29th November with the Twenty20 match in Dhaka but the Pakistan Cricket Board (PCB) have announced no further changes to the squads.
Pakistan Test squad: Misbah-ul Haq (captain), Mohammad Hafeez, Imran Farhat, Shahid Afridi, Younus Khan, Umar Akm, Shoaib Malik, Sarfraz Ahmed, Saeed Ajmal, Abdul Rehman, Umar Gul, Aizaz Cheema, Mohammad Khalil, Sohail Tanvir, Abdul Razzaq, Asad Shafiq
Pakistan One-Day International squad: Misbah-ul-Haq (captain), Mohammad Hafeez, Imran Farhat, Umar Akmal,, Abdul Razzaq, Shahid Afridi, Younus Khan, Asad Shafiq, Shoaib Malik, Sarfaraz Ahmed, Mohammad Khalil, Aizaz Cheema, Sohail Tanvir, Saeed Ajmal, Abdul Rehman, Umar Gul
© Cricket World 2011
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