Aiteo Cup holders FC Ifeanyi Ubah defeated Niger Tornadoes 1-0 in Nnewi on Thursday in their semi-final second leg, but still lost out 4-3 on aggregate after their shock 4-2 defeat in the first leg.
Godin Obaje's 85th minute penalty wasn't enough for the holders, who threw away a two-goal lead in the first leg in Lokoja.
Tornadoes stymied their opponents for much of the contest to set up a final showdown with either Akwa United or Sunshine Stars, who meet in the second leg of their double-header in Uyo on Sunday.
FCIU coach Yaw Preko welcomed back Nigeria B international defender Stephen Eze and Isaac Loute, but was missing Prince Aggrey as he looked to overturn the first-leg deficit.
The home team was quickly on the attack as they sought to find a way back into the contest, and Tornadoes had two players booked inside the opening 19 minutes as they struggled to deal with the pressure.
Loute missed the first big chance of the game in the 28th minute, failing to compose himself when presented with a decent opening.
Ifeanyi Ubah eventually got their goal late on when substitute Bright Onyedikachi was fouled by Isah Hussaini in the penalty box and Obaje coolly converted the ensuring spot kick.
However, the visitors defended resolutely in the final minutes of the game, holding out to qualify for a first final since they won the cup in 2000.