Both countries have been told they could face points deductions or even elimination from the competition if there is a repeat of the trouble.
"Both Bosnia-Herzegovina and Poland have been warned as to their future conduct," world football's governing body said in a statement.
"Should incidents of such gravity occur again, harsher sanctions, such as a points deduction or elimination of the representative team from a respective tournament, will be imposed by the FIFA Disciplinary Committee."
Bosnia were fined 50,000 Swiss francs after fireworks landed on the pitch during their match against Belgium in Genk and forced play to be halted.
"Between 45 and 50 fireworks were set off by the Bosnian supporters, with a large number landing on the pitch," said FIFA.
"The match had to be interrupted for eight minutes and the teams sent back to the changing rooms. A Bosnian supporter also invaded the pitch during the game."
Bosnia won the European Group Five match 4-2.
Poland were fined 25,000 after similar incidents during their visit to Belfast to play Northern Ireland.
"Polish supporters set off a number of fireworks at the beginning of the match, five of which were thrown onto the pitch. Later in the same match, police had to enter one of the Polish supporters´ areas of the stadium and had various objects thrown at them," said FIFA.
Meanwhile, Greece were fined 25,000 Swiss Francs after lasers were used and political banners displayed by supporters at their World Cup qualifier at home to Israel on April 1.
The statement reiterated that future World Cup qualifiers will be delayed if there are security problems, including outside the stadium.
