The Switzerland pair are both of ethnic Albanian heritage and celebrated their goals by making a gesture which seemingly symbolised the double-headed eagle on the Albanian flag.
Krstajic was left furious when referee Felix Brych failed to award a penalty in the 66th minute after Mitrovic was wrestled to the ground in the penalty area and criticised the German's decision.
"We were robbed," Krstajic told Serbian reporters on Saturday, when asked about Brych's decision. "I wouldn't give him either a yellow or red card, I would send him to The Hague. Then they could put him on trial, like they did to us."
Krstajic also posted photographs from the match on his Instagram account, accompanied by the caption: "Unfortunately, it seems that only the Serbs are condemned to a selective justice, once [it was] the damned Hague and today in football the VAR..."
The Hague-based International Criminal Tribunal for the former Yugoslavia was a United Nations body that prosecuted the perpetrators of war crimes committed during the wars in the former Yugoslavia.