The two former champions were the biggest casualties in the Cup competition.
After 90 minutes, four-time Cup winners Dolphins fired blanks against National League side, Akwa Starlets but went on to lose on 2-4 penalties in Umuahia while Kaduna United known as the Crocodiles slumped to a 1-2 loss to end their Cup dream.
Akwa Starlets had also accounted for the exit of another Premier League club, Kwara United, in the round of 64 in June.
Gbolahan Salami's early goal was enough for 3SC to dump out Juth while Cup holders, Heartland, edged out non-league outfit, Ingas FC via Bright Ejike's goal.
Enugu Rangers defeated Samba Kurna 2-0 through Oghogho Oduokpe's double.
In Ilorin, Nasarawa United romped to the biggest win in the round of 32 over City Of David (COD) United by 4-0.
Victor Namo scored twice while Dajang Wash and Habu Mohammed completed the rout.
Two goals from Alaba Osawe and Dayo Ojo set Sunshine Stars on the path of victory over Nembe City who pulled one back through Emmanuel Lashima.
Enyimba were made to work for their place in the last 16 in Lokoja by Remo Stars.
Jamiu Coker put Remo Stars in front on 38 minutes but a comeback from the People's Elephant in the last 20 minutes ended any hope of the Stars causing a major upset.
Bobby Sokari scored in the 70th minute and substitute Andrew Abalogu saw off Remo Stars' resistance with five minutes to time.
Anthony Okpotu and Nanen Imenger scored for Lobi Stars in their 2-0 win over Mountain of Fire Ministries (MFM) FC in Nnewi.
Federation Cup Round of 32 Results
Juth FC 0-1 3SC
Heartland 1-0 Ingas FC
Julius Atete FC 0-0 Sharks (6-7 pen)
Akwa United FC 1-0 Makwada FC
Enugu Rangers 2-0 Samba Kurna FC
Plateau United 0-0 Niger Tornadoes (5-6 pen)
Warri Wolves 1-0 Spotlight FC
El-Kanemi Warriors 1-2 Kano Pillars
FC Taraba 0-2 Gombe United
Nasarawa United 4-0 COD United
Nembe City 1-2 Sunshine Stars
Remo Stars 1-2 Enyimba
Dolphins 0-0 Akwa Starlets (2-4 pen)
Abia Warriors 2-1 Kaduna United
ABS 0-0 Bayelsa United (5-4 pen)
MFM FC 0-2 Lobi Stars