Football's global governing body said it was filing civil proceedings in South Africa against the company behind the campaign.
A criminal case has also been started against two women alleged to have masterminded the stunt.
On Wednesday, Barbara Castelein and Minte Immy Niewpoort appeared in the Johannesburg magistrate's court and were charged with contravening the South African Merchandise Marks Act. The two women were released on 10,000 rand bail (£891) and had their passports confiscated. They are due to reappear in court on 22 June.
They were part of the 36-strong group of women dressed in orange mini-dresses at the Holland-Denmark game on Monday. The dresses are associated with the lager brand as they are currently free with packs of Bavaria beer in Holland.
It is against FIFA regulations to promote any brands other than official sponsors during the World Cup games, and South Africa passed laws ahead of the World Cup to protect FIFA against such activity.
The same beer company pulled a similar stunt in the 2006 World Cup in Germany when a group of Dutch fans supporting Holland wore orange lederhosen advertising the beer brand. The fans were subsequently asked to strip if they wished to continue watching their team play.
Budweiser is the official beer sponsor of the 2010 World Cup and was also the beer sponsor of the 2006 tournament.
A FIFA spokesman said: "The matter is now under criminal investigation, and the South African Police Service is proceeding as per the normal legislation. Simultaneously, FIFA is now filing civil proceedings in South Africa against the company that is behind this campaign."
Industry experts say however, that if FIFA comes down too harshly on the brewery, it could look draconian to football fans and whip up negative publicity.
According to David Ko, executive vice-president for Asia-Pacific at Waggener Edstrom Worldwide, its is very obvious that Bavaria's stunt has succeeded when considering the publicity the arrests have ignited, yet there is no reason to celebrate.
"FIFA was right to rigidly enforce the right of their sponsors, especially during this year's World Cup where major sponsors, including Visa, have expressed dissatisfaction with their return on investment," he added.
Ko goes on to say that when a stunt diminishes the marketing investment of a rival brand in a major event, that is theft. FIFA did not overreact, they did exactly what they are supposed to do to protect their sponsors' interests.
Ko's colleague Meilin Wong Sandberg, director of client development for Asia-Pacific, says guerilla marketing that takes place outside the official venues are fine but inside and within the jurisdiction of the organisers and its sponsors, its a legal offence.
"If FIFA doesn't take a heavy hand on ambush marketers, it will lose valuable partners like Visa, Sony, Coca-Cola, adidas, Emirates and Hyundai who essentially make major global tournaments like the World Cup possible," added Sanberg.
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