Swiss coach Vladimir Petkovic indicated after the win that he was unimpressed by Shaqiri and Xhaka's celebrations.
"Anyone who experience the electric atmosphere of the game can appreciate more the performance of our national team and can understand the emotions which overcome a player", Defence, Civil Protection and Sports minister Guy Parmelin told the Neue Zurcher Zeitung (NZZ).
The two goal scorers have ethnic Albanian heritage linked to Kosovo, a former Serbian province that declared independence in 2008.
After falling behind in the fifth minute, Switzerland defied a cauldron-like atmosphere created by fervent Serbian supporters as they hit back with a thunderbolt from Xhaka and a last-minute breakaway goal from Shaqiri.
Federation Internationale de Football Association outlaws all political messages or symbols in stadiums and the three players could have been banned for up to two games if they were found to have breached rules.
Socialist lawmaker Geraldine Savary described the rhetoric on the right as "a shame", given the "happiness" both players had brought to Swiss fans.
"I just said how I felt about this, and that is the referee has severely damaged us in various parts of the game", Tadic said.
NZZ described Shaqiri and Xhaka as the Switzerland's two most talented footballers of their generation but said they "should have let the football speak for itself".
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After scoring, both made an eagle gesture understood to symbolize the two-headed eagle on the Albanian flag.
Meanwhile, the Serbian papers also slammed what they labelled "shameful provocation" by Shaqiri and Xhaka.
Shaqiri said: "It's nothing to do with politics, it's about football".
Even a draw would be enough on Wednesday for the Swiss in their final Group E match against Costa Rica, which lost its first two games and has already been eliminated.
Shaqiri was born in Kosovo and plays with the Kosovan flag stitched into his boots.
"We are not clear how the German referee could have been appointed for the match between Switzerland and Serbia, when it is well known that one of Swiss confederation cantons is a German canton", Serbia said in its statement.
"At the World Cup we support Switzerland and we play for Switzerland".
Serbia boss Mladen Krstajic said when asked if he had any comment to make about the celebrations: "I don't have any comment".