Media reports after the match stated that sections of the home and away support engaged in anti-Serbian chants during the game, which was played in Albania and classified as a home match for Kosovo.
In addition to the fine, which equates to just over £41,000, the Croatian federation said it had also been given a warning by the game's world governing body that more stringent sanctions may follow if there were any further disturbances.
Croatia must play their home qualifier against Iceland on November 12 behind closed doors as the second part of a supporter ban imposed for previous disturbances.
FIFA's recent crackdown on misconduct by fans has also resulted in fines for the FAs of Albania, Argentina, Brazil, Chile, Estonia, Iran, Kosovo, Paraguay and Ukraine.
Like Croatia, Albania was fined £41,000, new FIFA members Kosovo £25,000, Brazil £21,000, Estonia and Paraguay £16,000, with Argentina, Chile and Ukraine all getting £12,000 fines.
These punishments were dished out by the disciplinary committee because of incidents in recent World Cup qualifiers and relate to "discriminatory and unsporting conduct by fans, including homophobic chants in some instances".
Iran's FA, however, was fined £37,000 for what FIFA described as "several religious manifestations during a match".
The disciplinary committee reached its decisions after analysing reports from the anti-discrimination match observers, match officials and relevant FAs, as well as looking at media footage.
FIFA added that in some cases mitigating circumstances, such as the FAs' efforts to raise awareness of discrimination, were taken into account.