Lobi Stars were beaten 6-5 on penalties by Apa United after the game ended 1-1.
Enyimba, 2005 champions succumbed to Abia Warriors, with Chisom Chikara's goal enough to separate the sides.
In Edo State, crowd violence ended what would have been another upset as Bendel Insurance fans invaded the pitch and assaulted the referee with minutes to the end of their match against Dynamites FC.
Defending champions Dynamites were leading when irate Insurance fans invaded the pitch and set on centre referee, Sam Agbagbatu.
The referee was rescued by police and taken to hospital.
Niger Tornadoes joined Enyimba and Lobi, losing to their Feeder Team by a lone goal, but Kwara United had no such problems in Ilorin where they overcame the challenge of ABS 1-0.
In Katsina, Spotlight FC defeated Dan Buram 2-1. Gateway United defeated Remo Stars 3-1 in the Ogun State final, while 3SC beat Crown in Oyo State.
Court of Appeal beat NAF Rockets 3-2 via penalty shoot out to win in Abuja after it finished 1-1 in regular time.
It was goals aplenty in the Ondo State final with Sunshine Stars having to come from behind twice before finishing on the right end of a 4-2 result over Tiwa Warriors.
Tiwa Warriors went in front early in the game, but Ajani Ibrahim equalised for the 2012 CAF Champions League semi-finalists.
The Warrriors then took the lead again but Godfrey Oboabona's penalty again pegged them back.
Sunshine then went ahead for the first time in the game through another penalty kick, before adding the icing on the cake late on.
Lagos was treated to what was tagged the Holy Ghost Derby, with church-owned clubs City of David, owned by the Redeemed Christian Church of God parish of the same name, squaring up against Mountain of Fire (MFM) FC.
The game went to penalties and COD triumphed 3-1, although MFM were left aggrieved about a disallowed goal they thought should have been allowed to stand.
All the state finalists qualify for the national FA Cup.