Plateau United put up a good fight but later succumbed to a dying minute controversial penalty to lose 0-1 to Esperance of Tunisia.
The home team was awarded a controversial penalty 10 minutes from time by the Egyptian center referee.
An Esperance player was fouled about two meters away from the penalty area but the center referee pointed to the spot.
Ben Romdhane beat goalkeeper Suraj Ayeleso to send the home supporters into wild jubilation.
Ayeleso was in superb form as he made several superb saves in the game.
The two legs ended in a 2-2 draw, but Esperance progressed on the away-goal rule.
The result meant the Jos side would drop to the Confederations Cup round of 32.
Nigeria’s other representative in the competition Rivers United will confront defending champions Wydad Athletic Club of Morocco on Sunday.