A lone goal from defender Joseph Yobo, his second in two matches, once again helped the Super Eagles to pick up three points.
The three other teams of the group, South Africa, Equatorial Guinea and Sierra Leone, all trail Nigeria by six points.
In another of the day's games Cape Verde beat Mauritius 1-0 in Group 1 with a penalty from their Spanish-based striker Dady.
Cape Verde stay within a point of group leaders Cameroon.
Meanwhile, in Group 7 the 1-1 draw between Madagascar and Mozambique was delayed for ten minutes when a last-minute penalty sparked uproar from the away side.
Madagascar's Guy Hubert Mamihasindrahona converted the spot kick, but Mozambique's players felt the decision had robbed their side of a win.
Both teams still trail Botswana and Ivory Coast in the standings who each have five points.
Lesotho lost 1-0 at home to Libya in a match played in Bloemfontein, South Africa.
Liberia's draw with Senegal was played in the Samuel K Doe stadium
The victory means Libya go joint top with Ghana; the Black Stars remaining Group 5 leaders on goal difference.
Zambia drew away to Swaziland in Group 11 in a result that keeps the three-team table wide open.
Meanwhile, Liberia completed an improbable comeback against Senegal in Monrovia.
In the first qualifier to be played in the country since 10 fans died attending the last Lone Star's game in June, Liberia scored two late goals to earn a 2-2 draw in Group 6.
The result leaves Liberia rooted to the bottom with two points from three games while Senegal top the group with Gambia on five.
In Saturday's games Egypt were facing a disappointing draw in Malawi until things got even worse for Hassan Shehata's team in Blantyre.
Chiukepo Msowoya's volley in stoppage time at the end of the game sparked celebrations across Malawi, but gloom in Egypt.
The reigning African champions now lie third in their group, and face a tough battle to reach the next phase.
Ghana may be the second best team in Africa at the moment, according to the Fifa rankings, but that did not count for much when they encountered Gabon in Libreville.
Michael Essien was in the Ghana team beaten by Gabon
The Nations Cup hosts from earlier this year had a strong side on display, but were not able to continue their good start to the campaign.
2006 World Cup finalists Angola - who host the 2010 Nations Cup but must still try to qualify for South Africa - went to Kampala and were beaten 3-1 by a triumphant Uganda.
Angola though do still retain the advantage in their group.
South Africa face the opposite challenge - they host the 2010 World Cup but must still qualify for the Nations Cup.
That task was made more difficult when they went down 1-0 to Sierra Leone in Freetown - just reward for some strong performances by the Leone Stars.
Rwanda are the surprise front-runners in Group 8, after a thumping 3-1 win over Morocco.
Cameroon, the best team in Africa according to Fifa's rankings, were furious with their goalless draw in Tanzania and Ivory Coast had to come back from a goal down to secure a draw against Botswana.
You can get more details on all the games using the links on the right hand side of the page, and tune in to Fast Track on the BBC World Service at 1600 GMT on Monday for more analysis of all the weekend's action.
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