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The 26-year-old fast bowler failed to get a wicket in his last five one-day internationals, including three Asia Cup matches in September last year.
He was left out of Pakistan's last series against New Zealand, but was redrafted for the one-day side on the back of good form in the ongoing Test series in South Africa.
The Pakistan Cricket Board (PCB) said there were five changes from the Test side, which is presently in Johannesburg preparing for the third and final Test starting from Friday.
"Asad Shafiq, Azhar Ali, Haris Sohail, Mohammad Abbas and Yasir Shah have been replaced by Mohammad Hafeez, Shoaib Malik, Hussain Talat, Usman Shinwari and Imad Wasim, respectively," said a PCB release.
Chief selector Inzamam-ul-Haq said the squad was selected with the World Cup - to be held in England from May 30-July 14 this year - in mind.
"While selecting the squad, we have tried to maintain consistency, taking into consideration player performances in white-ball cricket as well as looking ahead to the upcoming ODI challenges, including the World Cup," he said.
Amir's strong performance in the Test series made him an "automatic selection", said Inzamam.
There were no places for allrounder Haris Sohail - who returned from South Africa without featuring in the Tests due to a knee injury - and fast bowler Junaid Khan.
Batsman Shan Masood and allrounder Hussain Talat earned maiden calls for one-day internationals.
The five-match series starts in Port Elizabeth on January 19, followed by matches in Durban (January 22), Centurion (January 25), Johannesburg (January 27), and Cape Town (January 30).
Squad: Sarfaraz Ahmed (captain), Babar Azam, Faheem Ashraf, Fakhar Zaman, Hasan Ali, Hussain Talat, Imad Wasim, Imam-ul-Haq, Mohammad Amir, Mohammad Hafeez, Mohammad Rizwan, Shadab Khan, Shaheen Afridi, Shan Masood, Shoaib Malik, Usman Shinwari.
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