Arsenal midfielder Granit Xhaka and Stoke City forward Xherdan Shaqiri were fined £7,600 for making hand gesture to mimic the Albanian national symbol, an eagle.
New Arsenal signing and Switzerland captain Stephan Lichtsteiner was also fined £3,700 for his part in the goal celebrations, which saw their side leapfrog Group E rivals Serbia into second place after two matches.
Xhaka and Shaqiri are of Kosovar heritage and their celebrations greatly angered Serbia's FA, with their president condemning and claiming a "brutal robbery" had denied the Balkan side of a win last week .
FIFA had opened disciplinary proceedings against the Swiss players in the immediate aftermath and the trio have been warned over their "unsporting behaviour contrary to the principles of fair-play" in future matches. If the offence is repeated, the trio have been told they will face more severe sanctions.
Despite being recognised by UEFA, Serbia does not acknowledge Kosovo as an independent state, with relations between the Balkan nations remaining tense.
Swiss national team delegate Claudio Sulser said of the fines: "We take note of the decision and are happy that we can now focus solely on football."
FIFA also punished Slavisa Kokeza, Serbia FA president, and coach Mladen Krstajic in relation to comments they made on the goal celebrations after the match.
Kokeza and Krstajic were sanctioned with fines of £3,800 and both men were also warned about their conduct.
Serbia's FA was also fined £41,000 ($54,000) and given a warning "for the display of discriminatory banners and messages by Serbian supporters as well as for throwing objects during the match".
Switzerland face Costa Rica in their final Group E fixture on Wednesday requiring a point to qualify for the last 16.