"The Fifa Disciplinary Committee has opened disciplinary proceedings against the Swiss players Granit Xhaka and Xherdan Shaqiri for their goal celebration during the match Switzerland vs. Serbia", Fifa said in a statement sent to journalists on Saturday.
The Swiss came from behind to record a 2-1 win over the Serbians on Friday and boosted their chances of qualifying for the last 16.
Both players trace their roots to Kosovo, a former province of Serbia where thousands were killed and tens of thousands more chased from their homes during a 1998-1999 conflict between Serbian forces and ethnic Albanian guerillas.
After scoring against Serbia on Friday the players appeared to make an eagle symbol with their hands alluding to the double-headed eagle on the Albanian flag.
Shaqiri, 26, was born in Kosovo, which has an ethnic Albanian majority.More news: World Cup qualifying scenarios for every team before final group games
"It's just emotion", Shaqiri said of his celebration.
The game already has generated controversy centred on nationalist hand gestures made by Switzerland players Granit Xhaka and Xherdan Shaqiri following their goals. The Swiss flag is on his other shoe. It was a message for all the people who have supported me and stayed by me.
Shaqiri and Xhaka were also backed by Swiss captain Stephan Lichtsteiner. "They [players] used to be Kosovo Albanian refugees", he said on Twitter.
In a statement posted on its website Sunday, the Football Association of Serbia said it submitted to FIFA "seven videos that clearly showed tendency in officiating of the referee Brych to the detriment of our national team". It was hard for us Swiss and for the dual citizens it was even tougher.
He said: "I think in football you have always emotions".More news: Blast at Addis Ababa rally for new Ethiopian prime minister - Reuters witness
"It's clear that emotions surface. It was a provocation, we were playing against Switzerland, not Kosovo", team official Jovan Surbatovic told Serbian state-run broadcaster RTS.
Xhaka and Shaqiri are of Kosovar heritage and their celebrations greatly angered Serbia's FA, with their president condemning and claiming a "brutal robbery" had denied the Balkan side of a win last week .
"I think we all together need to steer away from politics in football and we should focus on this sport as a handsome game and something that brings people together".
Swiss coach Vladimir Petkovic after the match reproached the players, saying that soccer and politics should "never mix".
Swiss Foreign minister Ignazio Cassis was also sympathetic.More news: Mexico fans celebrate second consecutive win in World Cup