In Bauchi, Enyimba FC defeated Samba FC courtesy of a brace from Samuel Tswaya, while Rasheed Olabiyi sealed the 3-1 win for the former African champions.
The loss signaled the end of Samba's fairytale run in the competition as they also lost their first Group A encounter against Lobi Stars yesterday by 1-0.
A brace from Gambo Mohammed helped kano Pillars come from a goal down to beat Kwara United 2-1 in Lagos. In the aftermath of the loss, Kwara United have handed their Technical Adviser Tunde Sanni an indefinite suspension and have asked his assistant, coach Alli Zubair to take over in acting capacity.
In the other Group B game Crown FC and Kelechi Emetole's El Kanemi Warriors played out a goalless draw.
In Ibadan, NPL veteran striker Victor Ezeji and Gomo Obduku were among the goals as Sharks FC knocked Nigeria Premier League leaders Rangers Int'l FC out of the Federation Cup in a 3-2 encounter.
Ugonna Uzochukwu and Chikeluba Ofoedu had pulled Rangers level, but a late penalty was scored by ThankGod Amaefule to send Rangers home and mark a bad day for the Enugu teams in the competition.
In the other Group C game NNL saide Prime FC became the first team to make to the quarter-final as they defeated Dynamite FC 2-1.
In Port-Harcourt, Heartland played out a 1-1 draw with Nasarawa United, and the other Group B game Gombe United and Plateau United ended with a similar scoreline.
Group A - (Bauchi)
Enyimba Int'l 3 vs 1 Samba FC
Group B - (Lagos)
Kano Pillars 2-1 Kwara United
El-Kameni 0-0 Crown FC
Group C - (Ibadan)
Prime FC 2-1 Dynamite FC
Sharks FC 3-2 Rangers Int'l FC
Group D - (Port Harcourt)
Heartland FC 1-1 Nasarawa United
Gombe United 1-1 Plateau United
Uche George Egbe