Both Xhaka and Shaqiri performed matching celebrations following their goals, interlocking their fingers in a gesture celebrating Albania.
It was a sweet victory for Shaqiri and fellow Swiss goalscorer Granit Xhaka, who along with team-mate Valon Belrami were booed relentlessly by Serbia's fans throughout. Shaqiri drew attention to his heritage last month by posting a photo of his boots, which feature the flags of Switzerland and Kosovo.
But tensions remain high between the two nations as Serbia does not recognise Kosovo as an independent state. "I am a man of sports, and this is what I'm going to stay being".
The coaches of Serbia and Switzerland only want to talk about football, not about an entrenched political dispute casting a shadow over their teams' World Cup showdown in Russian Federation.
A reporter asked Petkovic how he would discuss the issue with his players, and the coach sidestepped the question. "It's a wonderful atmosphere and a positive experience and that's what football should be about".
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She also worries that it's even more hard for families to pursue asylum claims while they are in federal detention. But Republicans said they were uncertain if either measure would have enough support to be approved.
Hoping to turn the game on its head, Switzerland made a change at the start of the second half as Mario Gavranovic made his first World Cup appearance.
Sommer was powerless, however, in the fifth minute when Nemanja Matic won the ball and found Dusan Tadic, whose cross was met with a soaring header from Mitrovic.
With their group destiny in their hands, Switzerland will wrap up group play against already-eliminated Costa Rica in Nizhny Novgorod on Wednesday, while Serbia will face Brazil in Moscow that same day.
Serbia almost had their second just before the half but Dusko Tosic's diving header from point-blank range skidded off his head to Nemanja Matic who couldn't react fast enough to finish the chance. Serbia, too often less than the sum of their parts, gradually prevailed over Costa Rica because of Aleksandar Kolarov's sumptuous free-kick and the eye-catching attacking thrusts of Sergej Milinkovic-Savic. 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.
Switzerland 2-1 Serbia, Shaqiri bags a late victor as Serbia concede one goal lead to suffer a 2-1 defeat.