The Kosovo War ended in 1999 and independence from Serbia was declared in 2008. Xhaka has joint Swiss and Kosovar nationality.
Meanwhile, papers in Kosovo praised the "extraordinary performance" of the two players. Shaqiri, who has flags of Kosovo and Switzerland on his shoes, was born in Yugoslavia, then moved to Switzerland when he was a child. Xhaka's brother Taulant plays for Albania's national side.
Switzerland's Xherdan Shaqiri celebrates scoring their second goal during the World Cup group E match between Serbia and Switzerland in Kaliningrad Stadium in Kaliningrad, Russia, on June 22, 2018. Even before kick-off, SVP member and political commentator Roger Koeppel branded the team "a seasoned troupe of foreign mercenaries with Balkan accents".
Meanwhile, Stephan Lichtsteiner has become the third Swiss player to be investigated over a goal celebration.
Xhaka, Shaqiri and Lichtsteiner would likely have been shown a yellow card at the time for their celebrations. Both players are closely connected to the region.
On Saturday, Fifa confirmed its disciplinary committee had opened proceedings against Xhaka and Shaqiri, adding: "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".
The players denied that their celebration was political.
"I don't have any concerns", Swiss soccer federation president Peter Gillieron said Sunday in an interview published by Swiss news website "20 Minutes". "My celebration was for the people who have always supported me".
"I just said how I felt about this, and that is the referee has severely damaged us in various parts of the game", Tadic said.
Swiss Foreign minister Ignazio Cassis was also sympathetic. "One can feel patriotic emotions towards the nation that one has chosen, without forgetting his homeland of origin", said Cassis, who only became Swiss at age 15 and gave up his Italian citizenship before joining the federal cabinet. Shaqiri had posted a photograph on Instagram of his playing boots, one with a Switzerland flag on the heel and the other with a Kosovo flag.