After Omega Roberts put the Lone Stars ahead on eight minutes in Paynesville, the Super Eagles responded quickly through goals from Emmanuel Igiebor and Ikechukwu Uche.
But the Nigerians could not hold their lead and Jabateh Oliseh levelled midway through the second half on a difficult pitch surface due to heavy pre-match rain.
The teams clash again in Nigeria during October and it would be a shock if the two-time champions failed to maximise home advantage and secure a place among the 16 finalists in South Africa next January.
Nigeria have not won the competition for 18 years and failed to reach the 2012 tournament last February after being held at home by Guinea in the final qualifier.
Eagles' coaches have been fired with alarming regularity and incumbent Stephen Keshi, captain of the 1994 trophy-winning team, has promised to resign if they fail to oust a country 21 places lower on the African rankings.
There was a goal feast in Omdurman with 2012 quarterfinals Sudan defeating resurgent Ethiopia 5-3 thanks to a late Mohammed El Tahir brace after the visitors had wiped out a two-goal deficit.
El Tahir converted a penalty six minutes from time and scored off the rebound when another spot kick was parried in the final minute of a clash between former Cup of Nations title holders.
Mudather Eltaib gave Sudan an early lead that Getaneh Kebede cancelled and Mohammed Bashir and Musaab Omer scored to give the Jediane Falcons a 3-1 half-time cushion.
Goals from Adane Girma and Seyoum Tesfaye had Ethiopia level midway through the second half before El Tahir tilted the odds in favour of Sudan making a third appearance in four Cup of Nations.
There was also plenty of drama in Freetown as Tunisia twice came from behind to hold Sierra Leone 2-2 and become favourites to emerge victorious from the two-leg tie.
Sheriff Suma gave the Leone Stars an eighth-minute lead they held until Fateh Gharbi equalised midway through the second half and Alhassan Kamara and Youssef Msakni exchanged late goals.
Mali, who exceeded expectations by finishing third at the 2012 finals behind Zambia and Ivory Coast, built a 3-0 lead in Bamako over Botswana courtesy of goals from Cheick Tidiane Diabate, Mahamodou N'Diaye and Modibo Maiga. – Sapa-AFP