The Serbian FA was penalised over a banner depicting its former province Kosovo as part of Serbia. Croatia was fined after its fans abused Canadian ethnic Serb goalkeeper Milan Borjan during the group match between the two.
The Croatian and Serbian football federations were fined by FIFA's disciplinary committee on Wednesday for incidents involving ethnic provocations at the World Cup.
FIFA fined the Croatians 50,000 Swiss francs (€50,580) after the team's fans verbally abused and taunted Canada goalkeeper Milan Borjan, who has ethnic Serb family ties.
The Serbian football federation was fined 20,000 Swiss francs (€20,230) for a political banner about neighbouring Kosovo displayed in the locker room before playing Brazil in the team's opening game.
The banner in Serbian colours showed a map of the country that included the territory of its former province, which has been an independent state for nearly 15 years, and the slogan "No Surrender".
Kosovo, which has a majority ethnic Albanian population, has been under NATO protection since 1999 and the withdrawal of the Belgrade troops under the command of strongman President Slobodan Milošević.
Although a number of countries -- including most EU member states, the UK and the US -- recognise its independence, Serbia continues to refuse to do so, along with the likes of Russia and China.
The Kosovo football federation formally complained to FIFA about the banner, which was hung over two Serbia players' lockers on 24 November.
FIFA said the charge against Croatia related to the "use of words and objects to transmit a message that is not appropriate for a sports event".
Canada's Borjan was born in a region of Croatia with a significant percentage of ethnic Serbs, one of the Balkan country's main minorities.
He and his family left their hometown Knin in 1995 when it was taken by Croatian forces during Operation Storm. The ethnic Serbs have fled on tractors, among other means.
During Canada's 4-1 loss to Croatia on 27 November, one banner displayed by Croatian fans used a logo of tractor manufacturer John Deere and changed the marketing slogan to target Borjan.
The fans also chanted "Borjan is an Ustasha," an ironic reference to Croatia's World War II fascist movement that led the so-called Independent State of Croatia or NDH, a Nazi German puppet state.
The NDH authorities ran concentration camps for Jews, ethnic Serbs, Roma and other minorities, including Jasenovac, which is considered to be among the ten largest camps in Europe.
FIFA also fined Saudi Arabia 30,000 Swiss francs (€30,350) for "team misconduct" after getting six yellow cards in games against Argentina and Mexico.