Omega Roberts of the Lone Stars opened scoring in the seventh minute of the encounter and added a second in the 66th minute to save the day for the Lone Stars.
Eagles striker, Nosa Igiebor scored the equaliser for Nigeria in 16th minute to set the pace for an enthralling encounter.
Ikechuchkwu Uche put the Eagles in front from the penalty spot on the 20th minute.
With the result, Nigeria stands a good chance of qualifying for the tournament with a two-away-goal advantage.
The Eagles will host the Lone Stars between Oct. 12, and Oct. 14, for the second leg of the qualifier to decide which country picks the ticket for the tournament to be held in January 2013.
Earlier in the other fixtures, reigning African champions, Zambia defeated Uganda 1-0 to keep alive their hopes of defending the title they won in January 2012.
Central African Republic beat Burkina Faso 1-0, while co-host of the 2012 edition, Gabon were held to a 1 all draw by Togo.
In the other results, Ghana beat Malawi 2-0, Sierra Leone played 2-2 with Tunisia, while Sudan Beat Ethiopia 5-3 and Mali defeated Botswana 3-0.
Also on Saturday, Cape Verde beat former African champions, Cameroon 2-0, while 2012 finalists, Ivory Coast survived an early scare to beat Senegal 4-2 in the tension soaked encounter.
The Game between DR Congo and Equatorial Guinea has been shifted by the Confederation of African Football (CAF) to Oct. 12. (NAN)