Switzerland were largely ineffective in the first half, but they came out after the restart with more intent, and Arsenal midfielder Granit Xhaka levelled proceedings with a bullet strike right out of the top drawer, while a late victor from Xherdan Shaqiri secured a vital 2-1 result for the Swiss.
Switzerland's Granit Xhaka celebrates with the controversial symbol after scoring a goal against Serbia.
The "double-headed eagle" celebration, adopted by Xhaka after his thunderous equaliser and Shaqiri following his decider - a double-headed eagle graces Albania's national flag - ensured that nobody could overlook the game's complex political dimension.
Xherdan Shaqiri's last minute victor capped an impressive comeback for the Swiss in an eventful Group E encounter in Kaliningrad after Arsenal midfielder Granit Xhaka levelled following Aleksandar Mitrovic's opener.
Shaqiri was born in Kosovo before it declared independence in 2008, something Serbia fails to recognise. Serbia are one of several nations who refuse to acknowledge it as an independent state with relations between the two countries remaining tense.
Xhaka was born to parents originally from Kosovo of Albanian heritage, and his father was jailed in the former Yugoslavia for campaigning for Kosovan independence.
And a preliminary investigation was opened against the team's manager, Mladen Krstajic, for alleged statements made in the aftermath of the Switzerland match.
Shaqiri, who plays for Stoke City, said after the match that "it's just emotion" when he was questioned about the way he celebrated his late victor. You can see what I did, and it's just emotion, and I'm just happy to have scored the goal.
"We think we were roughly injured in the 66th minute and we're sure to file a Federation Internationale de Football Association appeal", FSS secretary general Jovan Surbatovic said, the Telegraph reported. Xhaka's brother Taulant plays for Albania's national side.
Years of war in Balkans sent many families to western European countries, including Switzerland. You should always show respect, " Switzerland coach Vladimir Petkovic said.
Serbia had taken the lead in the Group E clash through Aleksandar Mitrovic but Xhaka equalised with a thunderous strike shortly after the break.
Switzerland's coach, Vladimir Petkovic, added: "You should never mix politics and football".
Either FIFA enforces an atmosphere of political neutrality at the World Cup or the image of football's most important tournament will forever be tarnished.
The win puts Switzerland into second place in Group E with four points, the same as Brazil.