Football's world governing body also removed flags emblazoned with company logos during Sunday's Group D match between Ghana and Serbia at the Loftus Versfeld Stadium in Pretoria.
"In fact there were mass ambush activities by one company from Ghana during yesterday's match and as per the regulations the FIFA Rights Protection team had to collect a few flags carrying heavy commercial branding," FIFA spokesman Nicolas Maingot said in an emailed response to Reuters.
"Most other flags where the branding was only very small were not taken away."
In April, Kulula, a local low-cost airline known for humorous advertisements, agreed to withdraw its tongue-in-cheek billboards after a legal letter from FIFA which was given wide media coverage here.
The advertisement called Kulula the unofficial carrier of the "You-know-what" and showed footballs, vuvuzela fan trumpets and soccer players.
FIFA makes most of its money, which has to last until the next World Cup in four years time, through selling television rights and deals with commercial sponsors.
More than 60 percent of FIFA's 2007-2010 revenue of $3.2 billion comes from TV rights and about 30 percent from commercial marketing.
