FIFA opened disciplinary proceedings against Swiss players Granit Xhaka and Xherdan Shaqiri on Saturday over their pro-Kosovo goal celebrations during the 2-1 win against Serbia.
Switzerland's scorers on Friday, Xhaka and Shaqiri, celebrated their goals by making a double eagle gesture with their hands to represent the Albanian flag.
Many people in Kosovo, which has an ethnic Albanian majority, identify with the flag.
Both players trace their roots to Kosovo, a former province of Serbia that declared independence in 2008 in a move that Belgrade still refuses to recognise.
FIFA bans all political messages or symbols in stadiums.
World football's governing body said it was also probing Serbia coach Mladen Krstajic for alleged statements made after the game.
Krstajic reacted to the defeat by calling for the match referee, Felix Brych of Germany, to be put on trial in a war crimes tribunal in the Hague for failing to award Serbia a penalty.
Serbia were furious when Brych failed to award a spot-kick in the 66th minute after Aleksandar Mitrovic was wrestled to the ground in the penalty area by Swiss defenders Stephan Lichtsteiner and Fabian Schaer.
Disciplinary proceedings have also been opened against the Serbian football association for crowd disturbances and the display of political and offensive messages by Serbian fans.
Xherdan Shaqiri (pictured) and Granit Xhaka, who both trace their roots to Kosovo, celebrated their goals against Serbia--whose government does not recognise Kosovo's independence--with a gesture referencing the Albanian flag