A rousing team talk from coach Vladimir Petkovic may have kicked his players into life, and it only took his men seven minutes to get the equaliser.
"Well, I will speak with the players and I will tell them we've had a great match against Brazil", he told a press conference.
Shaqiri clipped the post with a shot as Switzerland pushed on for a victor, but it was Serbia who felt hard done by shortly afterwards when Alexsandar Mitrovic was given the Harry Kane treatment, held down by both Fabian Schar and Stephan Lichtsteiner in the box only for the referee to wave away his claims for a penalty. The Swiss have dozens of ethnic Albanians in their national football program.
Xhaka and Shaqiri are among several members of the Swiss squad who are of Kosovar heritage, which added an extra dimension to the match. Relations between Serbia and Kosovo have remained fraught, as Serbia refuses to recognize its former province as an independent nation.
Swiss coach Vladimir Petkovic has vowed to keep up his side's high-tempo, physical approach that earned them a draw with Brazil. "We're here for sports to represent our country in the best possible way and we're not at all interested in anything else".
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However, after a six-month loan spell with Fulham, the striker hit insatiable form towards the tail end of the season - and just in time for the World Cup - as his goals helped the west London club clinch promotion to the Premier League.
Xhaka silenced the Serbian contingent in the 52nd minute, however, when he rifled home a loose ball in spectacular style from 25 metres before Shaqiri ran onto a through ball and finished with aplomb to win the game at the death.
Serbia coach Mladen Krstajic was equally reluctant to be drawn into the debate.
The win puts Switzerland into second place in Group E with four points, the same as Brazil. Shaqiri drew attention to his heritage last month by posting a photo of his boots, which feature the flags of Switzerland and Kosovo.
Such displays have angered some Serbian fans, who often wear T-shirts bearing the map of Kosovo with the Serbian flag on it.
Switzerland came right back into the game seven minutes after halftime thanks to Xhaka's fulminating strike after a rebound fell nicely into his path.