FIFA general secretary Jerome Valcke told a news conference the decision had been based on the world rankings and had no connection with the controversy over France's infamous "handball" goal against Ireland.
The top seeds are hosts South Africa, holders Italy, Argentina, Brazil, England, Germany, Netherlands and Spain.
NEWS: World Cup draw pots
France are left as the most dangerous floating team who could be drawn in the same group as any one of the top eight seeds.
The draw for the finals, being staged in South Africa from June 11 to July 11, will be made in a 90-minute television spectacular starting at 5pm GMT on Friday.
The 32 teams will be drawn into four groups of eight. Apart from the seeds, teams will be placed in pots which will largely avoid teams from the same continent meeting each other.
Pot 1 will comprise the eight top seeds with South Africa already sure to play in Group A and in the opening match at Johannesburg's Soccer City stadium on June 11.
The second pot will comprise eight teams from Asia, North and Central America and Oceania - Australia, Honduras, Japan, Mexico, New Zealand, North Korea, South Korea and United States.
The third pot will be the five other African countries and three remaining South American nations - Algeria, Cameroon, Chile, Ghana, Ivory Coast, Nigeria, Paraguay and Uruguay.
The final pot is made up of the eight remaining teams from Europe - Denmark, France, Greece, Portugal, Serbia, Slovakia, Slovenia and Switzerland.
Valcke said there had been an agreement within the organising committee to base the seedings on the FIFA world rankings for October.
He said this had been done with the agreement of UEFA president Michel Platini of France who was very keen, for the sake of fairness, for it to be done when European teams had all played the same number of qualifying games.
Valcke said this agreement pre-dated the infamous play-off in Paris when France scored an equaliser against Ireland after Thierry Henry had blatantly handled before setting up the William Gallas goal which put France into the finals.
There had been some media speculation that France might be "punished" by FIFA after widespread protests at the result from Ireland and beyond.
The decision on how the seedings and pot grouping work means that the seeded teams would most fear being drawn into a group which included the United States from pot two, Ivory Coast from pot three and France from pot four.
