Omid Mousavi gave Afghanistan the early lead in the 21st minute at Hisor Central Stadium, Hisor, Tajikistan.
Majid Aliyari equalized for Iran five minutes later.
Amir Hossein Hosseinzadeh put Iran ahead in the 36th minute.
Aliyari again found the net in the 64th minute to seal the win for Iran.
Iran will face India on September 1 and Tajikistan on September 4 in Group B.
Group A participants are Uzbekistan, Kyrgyzstan, Turkmenistan, and Oman.