Both players, who are ethnic Albanians and of Kosovar heritage, celebrated with a gesture which appeared to imitate the eagle displayed on Albania’s flag.
Serbia refuses to recognise the independence of its former province Kosovo, whose 1.8 million people are mostly ethnic Albanians, which broke away 10 years ago.
The players denied that their celebration was political.
Shaqiri said: “It’s nothing to do with politics, it’s about football.”
FIFA said it had also opened proceedings against the Serbian FA for crowd disturbance and the display of political and offensive messages by Serbian fans.
A preliminary FIFA investigation had been opened against Serbian coach Mladen Krstajic for "alleged statements made in the aftermath of the match", added the governing body.
Media reports quoted Krstajic as telling Serbian reporters that German referee Felix Brych, who denied his team a penalty, should be put on trial in The Hague, home of the United Nations' war crimes tribunal for the former Yugoslavia.
Switzerland beat Serbia 2-1 in the Group E match.