Xhaka scored a second-half equalizer, and Shaqiri scored the 90th-minute victor - and both celebrated with the two-headed eagle gesture.
If the football governing body concludes that the duo violated the rule, they could be banned for up to two games.
Arsenal midfielder Xhaka, 25, was born to Albanian parents who were originally from Serbia.
Xhaka's father spent three and a half years as a political prisoner in Yugoslavia, while Shaqiri was born in Yugoslavia before emigrating to Switzerland as a child.
He joins team-mates Granit Xhaka and Xherdan Shaqiri, who are the subject of disciplinary proceedings after making politically-motivated gestures during their celebrations.
The double eagle symbol represents the Albanian flag and is viewed a symbol of defiance in Kosovo, which declared independence in 2008 in a move that Serbia still refuses to recognise.
It is unclear what the investigation into Krstajic refers to, but in comments to Serbian reporters on Saturday, he said of match referee Felix Brych: "I wouldn't give him either a yellow or red card, I would send him to The Hague".
The pair, who both have Albanian heritage but grew up in Switzerland, turned Friday night's match around after Serbia had taken the initial lead.
Serbia's FA was also fined £41,000 ($54,000) and given a warning "for the display of discriminatory banners and messages by Serbian supporters as well as for throwing objects during the match".
Federation Internationale de Football Association has launched proceedings against the Serbian FA head Slavisa Kokeza, Serbia coach Mladen Krstajic, and Switzerland captain Stephan Lichtsteiner.
"We have a very important group game in Nizhny [Novgorod] on Wednesday and we want to do everything we can to make the game against Costa Rica successful". Shaqiri was more terse: "I do not play politics, I play football", he said.
The build-up to the match had seen exchanges between Serbian players and Shaqiri, who wears boots with the Kosovo flag displayed on one heel and the Swiss one on the other.