The two players, who are of Albanian-Kosovan heritage, put their hands together to form what looked like a double-headed eagle similar to the one on the Albanian flag following their goals in the Group E game.
Critics claim that the gesture is a nationalist symbol which risks inflaming tensions in the Balkans among Serbians - who do not recognise Kosovo's independence - and ethnic Albanians.
"The FIFA disciplinary committee has opened disciplinary proceedings against the Swiss players Granit Xhaka and Xherdan Shaqiri for their goal celebration during the match Switzerland vs. Serbia," FIFA said in an official statement.
"In relation to the same match, disciplinary proceedings have been opened against the Serbian FA for crowd disturbance and the display of political and offensive messages by Serbian fans.
"Furthermore, a preliminary investigation has been opened against the coach of the Serbian national team Mladen Krstajic for alleged statements made in the aftermath of the said match."