Azhar, along with former captain Mohammad Hafeez, initially refused to join the camp ahead of next month's limited-over matches in New Zealand but Pakistan Cricket Board (PCB) said the ODI skipper would stay on.
"Azhar Ali met the chairman PCB (Shaharyar Khan). He tendered his resignation," PCB said in a statement.
"The chairman didn't accept his resignation, Azhar Ali agreed and he will continue as captain," it added.
Amir, fellow fast bowler Mohammad Asif and former test captain Salman Butt served jail sentences in Britain after being found guilty in 2011 of various offences of corrupt behaviour.
Former captain Imran Khan has backed Amir's return to international cricket but test skipper Misbah-ul-Haq feared the bowler's comeback would prove a big distraction for the team.
According to local media reports, former captain Shoaib Malik has been assigned to guide Amir on his comeback.
(Reporting by Amlan Chakraborty in New Delhi; editing by Sudipto Ganguly)
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