The left-arm fast bowler, who suffered a ligament injury in his right knee during a test series in Sri Lanka last month, has been advised to take four to six weeks of rest.
"I have spoken with Shaheen and he is understandably upset with the news," chief medical officer Najeebullah Soomro said in a statement issued by the Pakistan Cricket Board.
"Although he has made progress during his rehabilitation in Rotterdam, it is now clear he will require more time and is likely to return to competitive cricket in October."
Afridi has travelled to the Netherlands with the team, who play their third and final one-day international in Rotterdam on Sunday, August 21st.
Pakistan will begin their Asia Cup campaign in Dubai with an August 28th blockbuster against arch-rivals India.
That will be followed by a seven-match Twenty20 home series against England.
The PCB expects Afridi to return to action in a tri-series in New Zealand in October before heading to Australia for the Twenty20 World Cup.
