Plateau United who lost the first leg 4-2 in Tunisia needed to defeat their opponents by two unreplied goals to advance to the group stage.
Plateau United knocked out by Etoile du Sahel despite 1-0 win
No Nigerian team will feature in the 2018 CAF Champions League group stage.
The hosts had a good start and Tosin Omoleye scored what would turn out to be the only goal of the game in the 25th minute.
Plateau United tried to find a goal to level the scoreline on aggregate and progress to the group stage on the away goals rule but could not as Etoile held on till the end.
Kennedy Boboye's side had earlier defeated Eding Sports 3 - 0 in the first leg and 1 - 0 in the second leg to progress to this round.
The result means that no Nigerian team will feature in the 2018 CAF Champions League after MC Algers beat MFM 6-0.
Plateau United will now join MFM, Enyimba and Akwa United in the CAF Confederations Cup play offs.
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