Xhaka, whose brother plays for Albania, ran to the touchline and locked his thumbs together with fingers outstretched to make what looks like the double-headed eagle on Albania's flag.
Xhaka and Shaqiri were each fined the equivalent of $13,500, while the Swiss team captain, who also made the gesture but is not of Albanian heritage, was fined half that.
Arsenal midfielder Xhaka and Stoke City's Shaqiri trace their roots to Kosovo, a former province of Serbia where thousands were killed and tens of thousands more chased from their homes during a 1998-1999 conflict between Serbian forces and ethnic Albanian guerillas.
They were fined 10,000 Swiss francs ($10,000) each for "unsporting behaviour contrary to the principles of fair-play" and warned, while team captain Stephan Lichtsteiner, who joined in with the celebrations, was fined 5,000 Swiss francs and given a warning, Federation Internationale de Football Association said.
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.
FIFA's disciplinary regulations state that players found guilty of provoking the public face a two-match suspension and Swiss Football Federation president Peter Gillieron said he was hopeful that the pair would be absolved.
When asked about his celebration Shaqiri said, 'It's just emotion. "And I think the main thing is that we were not able to finish our opportunities".
Serbia does not recognise Kosovo's independence and relations between the two countries remain tense in the wake of a war in the late 1990s. I'm very happy to score this goal.
The BBC reported that Krstajic was speaking to Serbian reporters about German match referee Felix Brych when he said: "I wouldn't give him either a yellow or red card, I would send him to The Hague".
"You should never mix politics and football".
Switzerland's Xherdan Shaqiri celebrates the win over Serbia (AP).
"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.