It was believed to be filmed by the governing body's independent anti-discrimination observers and reported to those responsible for policing bigotry in the stadium.
Thousands of supporters chanted the slur when Germany goalkeeper Manuel Neuer prepared to take a goal kick in the 24th minute of the World Cup match.
Mexico's federation has in the past appealed to fans to refrain from blurting out the slur and the effort was largely successful at last year's Confederations Cup in Russia.
But it seems to have picked up again with fans chanting it at matches from Mexico City to California and now Russia again.
They copped 12 fines during the World Cup qualifiers for using it and while the Court of Arbitration for Sport cancelled two of them, it also ruled the chant was "insulting" and left other fines in force.
It was at the World Cup qualifying rounds and the Confederations Cup where FIFA's 'three-step' anti-discrimination process for dealing with bigotry from stands was first trialled.
It allows officials to stop, suspend or abandon games.
The Mexican association has gone as far as running an educational campaign asking fans to stop using the word.
They tweeted a warning hours before the Germany game that those who chant the slur could find themselves barred from stadiums.
"In Russia, avoid being detained having your Fan ID taken away. Remember that you represent the best fan base in the world," read the tweet.
It included a photo with words translating to "DO NOT SCREAM 'PUTO'".
FIFA did not elaborate on the nature of the disciplinary proceedings and didn't say when a hearing would take place, according to The Guardian.
It has raised questions about the governing body's handling of the situation.
It is now being accused of failing to follow protocol in the handling of the homophobic chant against the German player.
The abuse was the first major test at the World Cup of FIFA's 'three-step process'.
The first step involves the referee stopping the game so a warning can be issued over the public address, which, if ignored, is then escalated to the match being suspended and eventually abandoned.
However, FIFA did not initiate the three-step process on Sunday.
Asked why, a spokesman told the Daily Telegraph: "A public announcement was prepared, but the chants ceased.
"After the match, and as an important step for further action, the incident was duly included in the match report, as well as the evidence produced by the anti-discrimination observers.
"Based on those reports, FIFA's disciplinary committee has opened proceedings against the Mexican FA."
FIFA began taking action over the "puto" chant after being condemned for failing to punish Mexico for it at the last World Cup in Brazil.
But Mexico aren't the only ones copping flak — a total of 56 disciplinary actions were issued to various football associations over homophobic chants during this year's World Cup qualifiers. They included Argentina, Brazil, Chile, El Salvador, Honduras, Panama and Peru.
FIFA additionally cited Colombia, Costa Rica, Ecuador, Paraguay, Uruguay, Greece, Hungary and Serbia once each for homophobic chants.
Only Chile and Honduras ended up with stadium bans, sparking calls for FIFA to increase the severity of its punishments for homophobic chants.
Unlike "race, colour, language, religion or origin", sexual orientation is not mentioned in Article 58 of FIFA's disciplinary code, which governs discrimination, The Daily Telegraph reported.
All 56 cases of homophobic chanting during World Cup qualifying were dealt with under Article 67 of the code, which governs "insulting words", and for which there is no minimum tariff.
In November last year, Piara Powar, the chief of Fare, which helps FIFA administer its anti-discrimination monitoring system, said that "harsher punishments" were needed for homophobic abuse, highlighting the current loophole in the regulations.
