Serbia could still progress to the knockout stages, but they will likely need to defeat Brazil in their final Group E encounter.
"The gesture of Xhaka and Shaqiri causes hysteria in Serbia", the Zeri paper commented.
Shaqiri was born in Kosovo before it declared independence in 2008, something Serbia fails to recognise.
Both players have Kosovar roots and formed a double-headed eagle with their hands, which resembles the eagle on the Albanian flag.
The Serbian media called Shaqiri's goal gesture "shameful provocation".
A team that's not even at the World Cup scored today, not once, but twice.
Both their families had to take refuge in Switzerland during the Yugoslavia war of the 1990's. Mitrovic came close in the 19th minute when he controlled a cross from Branislav Ivanovic on his chest and sent a bicycle kick over the bar.
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Bates narrowly missed the highest individual score in this format though, falling short of Meg Lanning's 126 by just two runs. In reply, the visitors did not get off to an ideal start, losing three wickets for 22 runs inside the first seven overs.
Switzerland, who came to Russian Federation ranked ahead of the likes of France and Spain, felt their way into the game as the first-half progressed.
Die Nati nearly leveled matters on the half-hour mark.
Nemanja Matic missed a glorious chance to double the lead just before the break when Tadic's in-swinging corner found him unmarked at the back post but the Manchester United midfielder couldn't sort his feet out.
Matic said during the build-up the team were expecting a "hellish" encounter with the Swiss, who in their game with Brazil fouled star forward Neymar 10 times alone.
Xhaka pounced on the loose ball and unleashed a first time attempt from outs ide the penalty box which beat Serbia goalkeeper Vladimir Stojkovic with its pace and vicious swing before bulging the net.
This prompted Vladimir Petkovic to switch it up at half-time and he brought on Mario Gavranovic at the expense of a despondent Seferovic, and the Swiss attack was immediately transformed, as they pushed forward with more intent and goal than in the first half.
It looked to be heading for stalemate, before Switzerland broke and set Shaqiri free who slipped the ball past Serbian keeper Vladimir Stojkovic in the 90th minute.
The result leaves Serbia, Switzerland and Brazil in a three-way battle for the two qualifying spots from Group E. Switzerland and Brazil now top the group on four points, with Serbia on three.
"We expect FIFA to impose sanctions against the players who acted against rules of FIFA and fair play, as well as against the national association of the country they play for".