Both countries will now play their next home World Cup qualifiers without any supporters after the sides were found guilty of failing to control their supporters in recent matches
The two countries were reprimanded in January after incidents surrounding their supporters but had hoped that the world football's governing body would change their mind.
Hungary were punished after anti-semitic chants were heard during their World Cup qualifier against Israel in August while a group of Bulgarian fans shouted racist abuse at Denmark's Patrick Mtiliga in October.
Hungary will now play their World Cup qualifier against Romania in March without fans and on the same day Bulgaria's match against Malta will also be played out in an empty stadium.
Both countries have also been fined and have been warned that any further behaviour of a similar nature could lead to points deductions or disqualification from a tournament.