Some observers felt Scotland winger Ikechi Anya had been subjected to possible racist abuse from the home fans in the Philip II National Arena.
The campaigning group - Football Against Racism in Europe - announced the move on its Twitter account.
A brief statement read: "FARE has passed on to FIFA details of racism at the FYR Macedonia vs. Scotland FIFA World Cup 2014 qualifying match."
Anya's first few touches were jeered by the home fans, although other Scotland players also appeared to be booed during the visiting team's early spells of possession.
The jeers petered out as Scotland continued to dominate in the opening stages.
Anya went on to score the first goal in Scotland's 2-1 win and the visiting players were applauded off the park by many of the remaining home fans after celebrating with the away support.
Meanwhile, Scotland have slipped 13 places in the FIFA world rankings to 63rd spot.
The fall comes as a result of defeats to England and Belgium, who moved up four places to sixth.
The new list takes into account Scotland's 2-1 victory over Macedonia, who jumped 14 places to number 75 in the list.