Bosnia-Herzegovina supporters were found to have breached two Uefa regulations – throwing objects and racist and/or discriminatory behaviour.
The Bosnia-Herzegovina Football Federation has been fined 29,250 euros (£24,489) and ordered to partially close the national stadium for their next home game in a Uefa competition.
The national federations of Serbia, Estonia and Georgia have also been fined.
Serbia and Georgia will face partial stadium closures if they breach Uefa’s regulations again during a two-year probationary period, while Estonia have a one-year probationary period.
Panathinaikos have also been handed a suspended stadium closure for a two-year probationary period.
Uefa found the Greek side guilty on six charges, including “use of a laser pointer”, “throwing objects”, “discriminatory conduct” and “lighting of fireworks” during the 4-1 home Europa Conference League defeat to Chelsea on 24 October.
The club must also pay a fine of 76,000 euros (£63,631).