The players, who have ethnic Albanian heritage but grew up in Switzerland, put their open hands together with their thumbs locked and fingers outstretched to represent the double-headed eagle displayed on Albania's national flag.
The tabloid Blick took a similar line.
Shaqiri is now at the World Cup with Switzerland and is likely to resolve his future when his country exit the competition.
The players insisted there was nothing to see in their celebrations. "This is a victory for my family, for Switzerland, Albania, Kosovo". I can't discuss the gesture I'm afraid. "It was a really emotional game".
Swiss coach Vladimir Petkovic after the match reproached the players, saying that soccer and politics should "never mix".
The Serbian press meanwhile called Shaqiri's goal celebration "shameful provocation".
The two "celebrated their success with a "black eagle" sign of people who belive in the idea of the so-called "Greater Albania"," the online version of the Blic paper commented.
Mexico defeats South Korea 2-1
Son Heung-min pulled one back for South Korea in stoppage time with a spectacular left-foot strike from outside the area. Standing in Mexico's way is a South Korea side that was stifled by Sweden and fell 1-0 on a VAR-ruled penalty kick.
The Telegraph paper criticised the "provocative Albanian gesticulation" while the Vecernje Novosti, under the headline "Provocation of the Swiss", featured a large photo of Shaqiri's boots.
And so when Shaqiri walked out onto the pitch with the flag of Kosovo printed on one of his boots, he was booed by a section of Serbian fans.
"We sought that he changes the boots. It was a provocation, we were playing against Switzerland, not Kosovo", team official Jovan Surbatovic told Serbian state-run broadcaster RTS.
Kosovo President Hashim Thaci posted his congratulations to the Swiss team and the two scorers on Twitter, writing "Kosovo loves you!"
Petrit Selimi, a former high-ranking Kosovo government official, defended the players' actions. "They [players] used to be Kosovo Albanian refugees", he said on Twitter.
The use of the Albanian "crossed hands" symbol, which is also used by the Albanian football team to celebrate goals, could be read as a provocative act given Kosovo was a former province of their opponents Serbia - a country which has never formally recognised Kosovo's independence and which has attempted to prevent the fledgling nation from competing in sport at the global level.
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