There has been a debate in Pakistan cricket over giving Aamir a chance to redeem himself after he disgraced himself by getting involved in the 2010 spot-fixing scandal.
The players, including Ali and Mohammed Hafeez, had even refused to join the national camp, protesting Aamir's presence.
Ali today met Khan and requested that he be relieved of the duty to lead Pakistan but the former convinced him to continue as captain.
Aamir is one of the 26 probables named for Pakistan's pre-season conditioning camp. The young paceman served a five-year ban after being indicted in the scandal and was allowed to bowl in domestic cricket by ICC.
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Aamir had apologised to both Ali and Hafeez for his actions and had even offered to leave the game if they thought that he does not deserve to play for Pakistan again.
"I do respect their concerns but some of them, I told them, are not acceptable. So they understood and confirmed that they are on the same page with us," Khan had said.