The statement further read: "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".
After falling behind in the fifth minute, Switzerland defied a cauldron-like atmosphere created by fervent Serbian supporters as they hit back with a thunderbolt from Xhaka and a last-minute breakaway goal from Shaqiri.
Granit Xhaka of Switzerland celebrates after scoring his team's first goal during the 2018 FIFA World Cup Russia group E match between Serbia and Switzerland at Kaliningrad Stadium on June 22, 2018, in Kaliningrad, Russia.
The double eagle symbol represents the Albanian flag and is viewed a symbol of defiance in Kosovo, which declared independence in 2008 in a move that Serbia still refuses to recognise.
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 Russian Federation.
The goal celebrations of two Switzerland players is drawing the attention of Federation Internationale de Football Association, which is investigating the gestures by the players who are of Albanian-Kosovan heritage.
Shaq thinks LeBron James should forget about chasing championships
He famously left Cleveland for the Heat in 2011 and proceeded to reach the Finals in four straight seasons, winning two of them. But if I was him, I wouldn't be trying to get four, five and six because it ain't going to matter.
But there were earlier cases before Shaqiri and Xhaka's.
In 2012, Swiss television commentator Sascha Ruefer caused controversy with comments about an Xhaka miss during a World Cup qualifier against Albania, when Switzerland were already 2-0 ahead.
This is seen in Serbia as promoting the idea of a Greater Albania - a project that would see Albania's borders expanded to include parts of Serbia, Macedonia, Montenegro, and Greece.
"It's a special day for me", said Xhaka. Both players defended the celebrations as spontaneous and personal outpourings at moments of high-emotion, which may seem plausible given their opponent in Friday's match. "My celebration was for the people who have always supported me".
"You should never mix politics and football", he said. 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. Kosovo is mostly populated by Albanians.
Shaqiri - whose 90th-minute victor sparked wild scenes of celebration - was born in Kosovo, the former Serbian province that declared independence in 2008.