A stunning 2-1 result in Harare last time out gave the southern African minnows five points and an undefeated record from their three games.
Elsewhere, Togo are doing well to top Group Five, while Zambia's poor form continues as two home defeats have damaged their chances.
Group One
Only a last-minute goal by George Hummel for Namibia in Windhoek prevented Madagascar recording a second away win and joining Nigeria on seven points from three games.
Zambia, who were shocked at home by the islanders back in the opening match in September, continued to disappoint in a lacklustre 1-0 defeat by Nigeria in Lagos.
German-based Victor Agali got the only goal for the equally unimpressive Nigerians after Jay-Jay Okocha missed an early penalty, while the game was marred by the fatal shooting of a fan by a policeman outside the stadium.
1 Nigeria P3 GD 5-0 Pts 7; 2 Madagascar P3 GD 4-3 Pts 5; 3 Zambia P3 GD 3-4 Pts 3; 4 Namibia P3 GD 3-8 Pts 1.
Previous results
Nigeria 4-0 Namibia
Zambia 1-2 Madagascar
Madagascar 0-0 Nigeria
Namibia 1-2 Zambia
Nigeria 1-0 Zambia
Namibia 2-2 Madagascar
Group Two
It is already difficult to see beyond South Africa and Liberia in Group Two, although the Bafana Bafana's easy run to the finals took a stumble with a 1-1 draw in Mauritius, the first point for the islanders.
It should help South Africa to be in such a strong position because there is a growing tendency amongst their players, particularly those based in the Premiership, to want to miss out on matches which are deemed not critical.
Liberia emphasised their superiority over nearest challengers for second place, Congo, with a 5-1 hammering in Monrovia as the Lone Star benefit from George Weah's new coaching role.
1 South Africa P3 GD 5-3 Pts 7; 2 Liberia P3 GD 10-3 Pts 6; 3 Congo P3 GD 4-8 Pts 3; 4 Mauritius P3 GD 2-7 Pts 1.
Previous results
Liberia 4-0 Mauritius
Congo 1-2 S Africa
Mauritius 1-2 Congo
S Africa 2-1 Liberia
Mauritius 1-1 S Africa
Liberia 5-1 Congo
Group Three
Morocco took a huge step towards Mali 2002 when Abdeljelil Hadda's goal in the last round of matches inflicted a rare home defeat on Tunisia.
Gabon's challenge seems to have faded after a 2-1 defeat by an improved Kenya took the lustre off their opening 2-0 shock win over Morocco.
The East Africans will still probably need a rare away win in their return with Gabon next time out to have much hope of challenging the North African giants.
1 Morocco P3 GD 2-2 Pts 6; 2 Tunisia P3 GD 4-3 Pts 4; 3 Kenya P3 GD 2-2 Pts 4; 4 Gabon P3 GD 5-6 Pts 3.
Previous results
Gabon 2-0 Morocco
Kenya 0-0 Tunisia
Tunisia 4-2 Gabon
Morocco 1-0 Kenya
Tunisia 0-1 Morocco
Kenya 2-1 Gabon
Group Four
Burkina Faso are on course for their fourth successive finals, helped by their European contingent, especially young star Mamadou Zongo. They should top the group as they lead by two points and have already drawn in Algeria.
Burundi and Angola were always going to struggle to mount a challenge, and defeats in Algeria and Burkina respectively in the last round of matches has all but ended their challenge.
Angola have an outside chance, but will need to win their two remaining home games, and at least emulate their comeback from two down at home to Algeria.
1 Burkina Faso P3 GD 3-1 Pts 7; 2 Algeria P3 GD 5-4 Pts 5; 3 Angola P3 GD 2-3 Pts 2; 4 Burundi P3 GD 1-3 Pts 1.
Previous results
Burundi 0-0 Angola
Algeria 1-1 Burkina Faso
Burkina Faso 1-0 Burundi
Angola 2-2 Algeria
Algeria 2-1 Burundi
Burkina Faso 1-0 Angola
Group Five
The young Togo team top the table by a point after resilient 0-0 draws in Senegal and, most recently, in Guinea.
The group is still wide open, though, with Senegal retaining a good chance despite being bottom, as they have two home games left.
It could have been much better had they held on to an early lead in Uganda, but the rejuvenated Cranes levelled and are hoping to end years of under- achievement.
1 Togo P3 GD 3-0 Pts 5; 2 Uganda P3 GD 4-5 Pts 4; 3 Guinea P3 GD 2-3 Pts 4; 4 Senegal P3 GD 1-2 Pts 2.
Previous results
Uganda 3-1 Guinea
Senegal 0-0 Togo
Togo 3-0 Uganda
Guinea 1-0 Senegal
Uganda 1-1 Senegal
Guinea 0-0 Togo
Group Six
The real surprise package so far are tiny Lesotho, who are clearly benefiting from the experience gained by many of their players in South Africa.
Lesotho started by letting a 3-1 lead slip in the last ten minutes at home to Ghana, but more than made up for it with stunning displays to draw 1-1 at home specialists DR Congo and then shock Zimbabwe 2-1 in Harare.
Inconsistent Ghana followed their 4-1 thumping of Zimbabwe by losing 2-1 in Kinshasa to revive DR Congo's hopes, and will need to keep concentration to ensure they go through.
1 Lesotho P3 GD 6-5 Pts 5; 2 Ghana P3 GD 8-6 Pts 4; 3 DR Congo P3 GD 5-5 Pts 4; 4 Zimbabwe P3 GD 5-8 Pts 3
Previous results
Zimbabwe 3-2 DR Congo
Lesotho 3-3 Ghana
Ghana 4-1 Zimbabwe
DR Congo 1-1 Lesotho
Zimbabwe 1-2 Lesotho
DR Congo 2-1 Ghana
Group Seven
Egypt, winners of the Nations Cup in 1998, are on course to quickly wrap up their finals spot after not dropping a point or conceding a goal in their three matches.
A 4-0 thumping of Libya last time out, combined with a 2-0 victory for Ivory Coast over Sudan means Libya have to bounce back quickly in the return with Egypt at the end of March to retain any chance of catching the Elephants.
If the Ivory Coast fail to win in pointless Sudan, then the pressure of home support for Libya in Tripoli could just tip the balance their way.
1 Egypt P3 GD 6-0 Pts 9; 2 Ivory Coast P3 GD 4-2 Pts 6; 3 Libya P3 GD 2-6 Pts 3; 4 Sudan P3 GD 0-4 Pts 0.
Previous results
Egypt 1-0 Ivory Coast
Libya 1-0 Sudan
Sudan 0-1 Egypt
Ivory Coast 2-1 Libya
Egypt 4-0 Libya
Ivory Coast 2-0 Sudan