Babar stepped down as skipper in all three formats last year after Pakistan failed to make the knockout stage of the 50-over World Cup, before returning as white-ball captain in March for the T20 World Cup where his team didn't make the Super Eight.
The batting mainstay, as well as pace bowler Afridi, were left out of Pakistan's last two Tests against England, and the team wrapped up a 2-1 series win on Saturday.
The trio will not feature in the matches against Zimbabwe which follow the Australian series, however, as they will be rested.
Wicketkeeper-batsman Mohammad Rizwan will be available for the Australia games and the Zimbabwe ODIs, but will be rested for the T20s.
Pakistan play three ODIs and three T20Is against both Australia and Zimbabwe. The Australia tour runs from November 4-18.
Pakistan squads:
ODIs: Aamir Jamal, Abdullah Shafique, Arafat Minhas, Babar Azam, Faisal Akram, Haris Rauf, Haseebullah, Kamran Ghulam, Mohammad Hasnain, Mohammad Rizwan, Muhammad Irfan Khan, Naseem Shah, Saim Ayub, Salman Ali Agha, Shaheen Afridi.
T20Is: Arafat Minhas, Babar Azam, Haris Rauf, Haseebullah, Jahandad Khan, Mohammad Abbas Afridi, Mohammad Rizwan, Muhammad Irfan Khan, Naseem Shah, Omair Bin Yousuf, Sahibzada Farhan, Salman Ali Agha, Shaheen Shah Afridi, Sufyan Moqim, Usman Khan.
