Gernot Rohr included a few surprises in his starting XI, with Daniel Akpeyi preferred to Francis Uzoho in goal.
Paul Onuachu also started ahead of Odion Ighalo upfront.
However, the Super Eagles failed to make their dominance count, until Rohr introduced Ighalo in the second half.
The Shanghai Shehua striker ran onto a backheel from Ola Aina to net the winner.
Nigeria will take on Guinea in the next game on June 26.
