The Iranian Football Federation (IFF) was fined $3000 for throwing bottles by Persepolis fans in the match against Bunyodkor, ILNA news agency reported on Monday.
The reports said the IFF was fined because AFC regulations hold national football federations responsible for security at stadiums.
Persepolis lost its AFC Champions League match to Bunyodkor in May.
Knocking out Iran's last remaining team from the competitions allowed Bunyodkor to advance to the quarterfinals of the tournament.
Uzbekistan, China, Kyrgyzstan, Nepal and Thailand also saw their football federations fined based on decisions made during a September 29 AFC meeting.
The heaviest fine went out to Nepal's Football Association for stone throwing by fans at a match between Nepal and Kyrgyzstan during the AFC Challenge Cup Qualifiers.
Among the countries mentioned Thailand and Uzbekistan received the lowest fines — $1000 each.
Thailand was fined after a coach refused to take part in a post-match press conference and AFC decided to penalize Uzbekistan after spectators shone laser beams at the eyes of the opposing team's players.
AFC's penalties did not only go out to federations. The Saudi teams, Al-Hilal and Al-Ittihad, also received fines.
Several players and coaches from other countries were also fined and\or suspended.