On day one of the ongoing second Day-Night Test against Sri Lanka, Amir had hurt his right shin and returned to the dressing room towards the close of play on Friday. He was taken to the hospital on Saturday.
Amir has been advised two to three weeks rest after he underwent an MRI scan following complains of pain in his right shin.
The left-arm pacer will not bowl in the ongoing second Test at the Dubai Cricket Stadium but would be available to bat.
Amir's replacement in the ODI squad will be announced in due course.
The first ODI will be played at the Dubai International Stadium, Dubai on October 13, followed by games on October 16 and 18 at the Sheikh Zayed Stadium, Abu Dhabi.
The last two matches of the five-match series will be played at the Sharjah Cricket Stadium, Sharjah on October 20 and 23.
ODI Squad: Ahmed Shehzad, Fakhar Zaman, Mohammad Hafeez, Babar Azam, Shoaib Malik, Sarfraz Ahmed (C)(Wk), Imad Wasim, Shahdab Khan, Faheem Ashraf, Hasan Ali, Mohammed Amir, Ruman Raees, Junaid Khan, Haris Sohail and Imam-ul-Haq (ANI)