FC Taraba were without influential striker Luther Iyorhe who is still out injured, but Tochukwu Esom and Mohammed Abdulmalik got the nod to start upfront.
It was FC Taraba that dominated the opening half hour but could not make their chances count and their centre-back, Olabisi Samuel, will rue missing from close range.
Just before half time Esom benefited from a defensive mix-up by City and the FC Taraba man could only shoot wide from six yards.
At the break, it was clear FC Taraba had the upperhand, having created more scoring opportunities.
But it was Nembe City who took the lead just 14 minutes into the restart through John Eze's 25-yard free kick.
Minutes later, Eze nearly got his second of the afternoon but saw his goal-bound header cleared off the line.
FC Taraba head coach Ndubuisi Nduka did try to force the issue in Omoku by sending on Nura Ahmed and Bobby Abel for Abdulmalik and Fidelis Saviour respectively, but his tactics yielded nothing.
City finished the game strongly to earn their first full points of the season, but they still remain bottom with seven points after 10 matches.
In a Match Day 7 rescheduled game, Bayelsa United had to dig deep to defeat six-time champions Enyimba 2-1 at the Samuel Ogbemudia Stadium in Benin City.
Eric Frimpong scored the opening goal for Bayelsa United on 26 minutes and the celebration of his goal was hardly over when Abdulrahman Bashir put Enyimba on level terms two minutes later.
But it was ex-Prime FC defender Aniyikaye Adeleye who scored the winner for Bayelsa United at the death.
Bayelsa United are now fourth in the NPFL standings with 17 points while Enyimba are in ninth place with two points less.
Sunshine Stars also played themselves into the top-five with a two-nil win in their Match Day 3 rescheduled game over new boys Giwa FC.
Cameroonian midfielder Tamen Medrano and Dele Olorundare scored in the second half to secure a fourth win for the Akure Gunners.