Xhaka and Shaqiri, who are of Albanian-Kosovan heritage, both celebrated their goals with a gesture which appeared to imitate the eagle displayed on Albania's flag.
Serbia does not recognize the independence of its former province Kosovo, which broke away ten years ago and whose 1.8 million people are mostly ethnic Albanians.
According to the BBC, FIFA has opened disciplinary proceedings against the two players and will check their actions for consistency with the Article 54 of the FIFA Disciplinary Code "Provoking the general public" which states that anyone who provokes the general public during a match will be suspended for two matches and sanctioned with a minimum fine of CHF 5,000 [$5,062].
If found guilty, Xhaka and Shaqiri could miss their side's final World Cup group-stage match against Costa Rica.
Switzerland is second in Group E with four points and is set to face Costa Rica in their last group game on Wednesday. A win or a draw will put them through to the round of 16.
The 2018 FIFA World Cup kicked off on June 14 and will continue until July 15, with the matches being played in 11 cities across Russia.