This comes after their respective national associations announced that the nations would not be entering the preliminary competition, the world football governing body said on its website.
The first round of qualifying was scheduled to feature two-legged ties between the ten African member associations currently lowest in the FIFA/Coca-Cola World Ranking.
This included the twin islands of Sao Tome and Principe (which are one nation) and the Central African Republic.
In an effort to maintain the same format for the second round of African Zone qualifiers, and after discussions with the African Football Confederation, FIFA decided to award a first-round bye to the two highest-placed countries in the July 2007 edition of the rankings.
Swaziland and Seychelles, who share 147th spot, are the two beneficiaries.
As a consequence of this reshuffle, the opponents of the two teams to be given a bye will face now each other for a second-round berth.
Somalia and Djibouti, who were set to play Swaziland and Seychelles over two legs, will instead play a one-off qualifying match on 17 November.
After the withdrawals of Sao Tome and Principe and the Central African Republic, there will now be only three first-round ties rather than the five initially scheduled.
The first round of African Zone qualification matches will see Madagascar play Comoros (first leg - 13 October 2007, Second leg - 17 November 2007).
Sierra Leone will face off with Guinea Bissau (first leg - 14 October 2007, second leg - 17 November 2007) and Djibouti will play against Somalia (single match play-off in Djibouti, 17 November 2007).
All these matches will come ahead of the preliminary draw on 25 November 2007, in Durban South Africa.
This draw is part of the process to determine which qualifying international teams will play against each other in the world's biggest soccer tournament in less than 1000 days' time. -