Swiss coach Vladimir Petkovic said politics and football should "never mix" after his two players celebrated goals with the political gestures.
Granit Xhaka gave Switzerland an equalizer against Serbia in the 52nd minute Friday with a brilliant strike from long range - but the replays showed that the attempt at goal likely should have been blocked by Serbia's Branislav Ivanovic.
Xhaka struck the Swiss equalizer in the 52nd minute before Shaqiri scored a late victor when he broke free from the half-way line to slot past Serbian goalkeeper Vladimir Stojkovic.
Then Swiss midfielder Xherdan Shaqiri, who was born in Kosovo, scored the winning goal in the 90th minute of the game on a breakaway pass that led him charging down the field.
Kosovo gained independence from Serbia in 2008, however, Serbia still reject this.
Head coach Mladen Krstajic is not expected to make major changes but he could hand winger Filip Kostic a start. Serbia won their opening contest Costa Rica with skipper Aleksandar Kolarov scoring from a free kick. "We have our goals".
Shaqiri makes no secret at his pride for his heritage at the World Cup.
Xhaka was born to Kosovan-Albanian parents and has a brother, Taulant, who represents the national team. (Getty Images) Shaqiri had the Kosovo flag on his right boot against Serbia.
Valon Behrami formed another luxurious axis in the heart of Switzerland's midfield, building on the sensational performance he put in against Brazil on Sunday, as he anchored the middle of the park judiciously, bringing composure and assurance to the midfield.
Such displays have angered some Serbian fans, who often wear T-shirts bearing the map of Kosovo with the Serbian flag on it. There was, nevertheless, plenty for Serbia to be pleased about, with Mitrovic particularly impressive in the air.
Boasting one of the oldest defences in the tournament, Serbia's rearguard and goalkeeper have collectively racked up almost 300 caps between them, as defensive tyro Nikola Milenkovic is the only player in the Serbian backline below the age of 30.
Serbia were making all the forays in and around the offensive third.