Aleksandar Mitrovic helped Serbia to an early lead in Kaliningrad, but a long range strike from Xhaka shortly after half-time instigated a Swiss revival, before Shaqiri snagged a goal at the death to give Switzerland a 2-1 victory.
The duo's celebrations each featured a gesture depicting the Albanian Eagle shown on the nation's flag - a nod to their Kosovar Albanian heritage and direct message to their opponents.
Born in Kosovo, Shaqiri and his family fled to Switzerland during their home nation's war with Serbia in the late 1990s, and while Kosovo have since gained independence and become a FIFA-recognised national team, Serbia do not share such sentiments.
With Xhaka's family also seeking refuge in Switzerland, the celebrations aimed in the direction of the Serbian supporters have since been branded as an emotional response.
"I think about this, I don't want to speak," Shaqiri said after the match.
"In football, you have always emotions. You can see what I did, and it's just emotion, and I'm just happy to have scored the goal. I did it, and we don't have to speak about this."
Shaqiri had already incited backlash from the Serbia national team in the lead-up to Saturday's fixture after the Stoke City winger posted a picture of his boots emblazoned with the flag of Kosovo.
"If he loves Kosovo so much and decides to flaunt the flag, why did he refuse a chance to play for their team?" Mitrovic asked.
The political back-and-forth has since been addressed by Switzerland head coach Vladimir Petkovic.
"You should never mix politics and football," Petkovic said. "You should always show respect. It's a wonderful atmosphere and a positive experience and that's what football should be about."
Nevertheless, the win puts Switzerland in second place and one point ahead of Serbia with one match still left to play in the group stage.
