After scoring, both made an eagle gesture understood to symbolize the two-headed eagle on the Albanian flag.
It's the goal celebration that everyone is talking about at the World Cup, but not everyone is celebrating.
After the game, which his side won 2-1, Switzerland's Bosnia-born manager Vladimir Petkovic was asked about the celebrations and said: "You should never mix football and politics". "I'm very happy to score the goal, that's all".
But there were earlier cases before Shaqiri and Xhaka's. Each had scored in Switzerland's 2-1 victory over Serbia, whose crackdown on the Albanian population was ended by North Atlantic Treaty Organisation intervention in 1999. Shaqiri left when he was four years old.
The players, Granit Xhaka and Xherdan Shaqiri, have ethnic Albanian heritage linked to Kosovo, a former Serbian province that declared independence in 2008. Serbia doesn't recognize Kosovo's independence and relations between the two countries remain tense.
Xhaka and Shaqiri's behaviour divided opinions in Switzerland with some politicians defending them and others saying they felt their goals were scored by Kosovo rather than Switzerland.
In a statement posted on its website Sunday, the Football Association of Serbia said it submitted to FIFA "seven videos that clearly showed tendency in officiating of the referee Brych to the detriment of our national team".
"Switzerland gave my family everything, and I try to give everything for the national team". I am a man of sports and this is what I am going to stay. It is not something logical. "I was criticized for it, but it's insane to me that some people feel this way because it's simply my identity".
"It's clear that emotions surface. It's not more. I think we don't have to speak about this now".
Xhaka "shamefully provoked our fans", the online version of the Blic paper commented.
"We have always displayed pride as a defence mechanism, not really as something to poke into somebody's eye", said Ely Lokku, an ethnic Albanian originally from Macedonia who now lives in Toronto.
"Unfortunately we have not played like we did in 2014", coach Oscar Ramirez said.
Serbian newspapers also noted that Shaqiri had both Swiss and Kosovar flags on his shoes during the match.