Both men have roots in Kosovo, a former province of Serbia that declared independence in 2008.
When asked about the way he had celebrated, Shaqiri said in a post-match press conference streamed on FIFA's website: "I think in football you have always emotions".
Meanwhile, Stephan Lichtsteiner has become the third Swiss player to be investigated over a goal celebration.
The duo could miss Switzerland's crucial last Group E encounter against Costa Rica in Nizhny Novgorod on Wednesday (June 27) as the alleged offence carries an automatic two-match ban under FIFA's disciplinary rules. "After that, it was all Switzerland", said Djokovic, who faces Marin Cilic in the Fever-Tree Championships final on Sunday.
Morocco know their chances of extending their stay in Russian Federation have already been ended, with a pair of 1-0 losses against Iran and Portugal ensuring they will return home after this final group game.
Both are among the players in the Switzerland team who have links to Kosovo - Shaqiri wears boots with the Kosovo flag displayed on one heel and the Swiss one on the other. Each had scored in Switzerland's 2-1 victory over Serbia, whose crackdown on the Albanian population was ended by North Atlantic Treaty Organisation intervention in 1999. Serbia doesn't recognise Kosovo's independence and relations between the two countries remain tense.
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And Switzerland's coach, Vladimir Petkovic, added: "You should never mix politics and football".
Both players, who are ethnic Albanians and of Kosovar heritage, celebrated with a gesture which appeared to imitate the eagle displayed on Albania's flag.
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". "I think that's something that was expected already more than 10 years ago in football, and I don't know why they waited for so long, but it's refreshing to see it".
But Shaqiri, who was booed constantly by fans of Serbia throughout the match, put his use of the Albanian gesture down to the heat of the moment. "I told them I would not be content with a draw".
Both players are ethnic Albanians from Kosovo, where a Serbian crackdown on the Albanian population only ended with North Atlantic Treaty Organisation military intervention in 1999.