Granit Xhaka and Xherdan Shaqiri both made hand signals that appeared to imitate the double-headed eagle on the Albanian flag.
The pair, who have ethnic Albanian heritage and whose roots are in Kosovo, put their open hands together with their thumbs locked and fingers outstretched.
The thumbs represent the heads of the two eagles, while the fingers look like the feathers.
Football’s world governing body has begun disciplinary proceedings against the players over their apparent Albanian nationalist gestures.
It has also opened disciplinary proceedings against the Serbian Football Association for crowd disturbance and the display of political and offensive messages by Serbian fans. And it is reviewing statements that Serbia coach Mladen Krstajic made after the match.
Many people in the former Serbian province of Kosovo, which has an ethnic Albanian majority, identify with the red and black flag.
A Serbian crackdown on Kosovo Albanian rebels in 1998-1999 only ended when NATO intervened.
Kosovo declared independence in 2008 but Serbia does not recognise the status, and relations between the two countries remain tense.
The Serbian media called Shaqiri’s goal gesture “shameful provocation”.
The Serbian football association reportedly complained to FIFA before the game about the Kosovo flag on one of Shaqiri’s boots. The Swiss flag is on his other shoe.
“We sought that he change the boots. It was a provocation, we were playing against Switzerland, not Kosovo,” team official Jovan Surbatovic told Serbian state-run broadcaster RTS
Shaqiri was born in Kosovo, while Xhaka’s parents are originally from Kosovo. His brother plays for Albania’s national team.
