Alizadeh suffered an anterior cruciate ligament (ACL) injury during training for the second time in 13 months and now faces several months on the sidelines again.
On Tuesday, Iran's National Olympic Committee (NOC) chose Ahmadi as the new flagbearer in the Games.
Ahmadi, 36, is a four times Asian Games medalist having won three medals - two silvers and a bronze - at Guangzhou 2010 and a silver at Incheon 2014.
The 2018 Asian Games will be held in Indonesia from August 14 to September 1.