The preliminary round's opening legs take place on 6-8 January, two weeks before the 2012 Nations Cup begins.
Meanwhile, the return legs of those ties will take place on 20-22 January, the same weekend as the finals in Equatorial Guinea and Gabon kick off.
The scenario has arisen as the finals are moving from even years to odd ones.
This action has been taken by Caf to ensure that the Nations Cup, which has been played in even years since the 1965 finals, no longer clashes with the World Cup.
Meanwhile, the third and final round of qualifiers will take place in September and October.
Only four teams will enter preliminary round one, with Seychelles taking on Swaziland and Sao Tome meeting Lesotho - with the winners meeting DR Congo and Sierra Leone respectively in the next round.
The second round intensifies the race to qualify for the finals in South Africa, with 28 teams clashing home and away, albeit with four months separating the ties.
It is at this stage that some of African football's superpowers enter the field, such as former continental champions Egypt, Cameroon and Nigeria.
The third and final round of qualifying takes place in September and October, when the 16 teams who contest next month's Nations Cup enter the field.
Since 30 teams contest the final round, two finalists from Equatorial Guinea and Gabon must clash in this round.
Round 1: 6-8 January & 20-22 January 2012
Round 2: 29 February & 15-17 June 2012
Round 3: 7-9 September & 12-14 October 21012
Preliminary round one:
Seychelles v Swaziland
Sao Tome v Lesotho
Preliminary round two:
Ethiopia v Benin
Rwanda v Nigeria
Congo Brazzaville v Uganda
Burundi v Zimbabwe
Algeria v The Gambia
Kenya v Togo
Sao Tome/Lesotho v Sierra Leone
Guinea Bissau v Cameroon
Chad v Malawi
Seychelles/Swaziland v DR Congo
Tanzania v Mozambique
Central African Republic v Egypt
Madagascar v Cape Verde
Liberia v Namibia