The federation's disciplinary committee said in a statement Thursday it fined champion Viktoria Plzen and Jablonec 100,000 koruna ($4,110) each, ESPN FS reported.
In a match against Bohemians Prague 1905, Jablonec fans unveiled a huge poster with a female figure called "Europe" kicking a pig wearing a turban.
Police also have been investigating the case.
Plzen fans displayed a similar anti-Islam poster in a match against Slavia Prague.
The Czech Republic, which has a population of more than 10 million people, is home to around 15,000 Muslims.
In 2004, Prague acknowledged Islam as an official religion, giving Muslims rights on equal footing to Christians and Jews.
In April 2014, police forces raided the Islamic center on the Prague’s outskirts during Friday prayers, detaining 20 people and arresting a 55-year-old publisher of a book following accusations of inciting Xenophobia and violence.
Analysts warned that the raids might fuel anti-Muslim sentiments in the country at a time when the far right is gaining ground.
Later in January 2015, a Japanese-born Czech politician raised criticism after calling people to walk their pigs and dogs outside the country’s mosques.