Musa was looking unsafe and in the 38th minute, he skipped past his marker on the left wing and tried to cut inside past Ngadeu, but the burly Cameroonian defender halted his progress with a well-timed tackle.
Three minute later, Ighalo turned from goalscorer to provider with an excellent pass through Banana's legs to the path of Alex Iwobi to blast home the ball past Andre Onana for Nigeria's third goal on the night.
Both sides have had disruptions before and during the tournament, but this is knockout football - and there can be no excuses.
After netting a brace in Nigeria's 3-2 win over Cameroon on Saturday, Odion Ighalo has claimed his contributions were all about getting a win and not his goal tally.
In the 51st minute, the Indomitable Lions came close to extending their lead.
"We conceded two goals in a short time, we could collapse, but we tried until we achieved what we wanted".
Ahmed Musa will continue on the left flank while Odion Ighalo should lead the line, meaning Paul Onuachu and Samuel Chukwueze will remain on the bench.
Clarence Seedorf's side needed a victory to guarantee they progressed from Group F in first place but found a stubborn Benin side hard to break down in Ismailia and will now face Gernot Rohr's side in Alexandria on Saturday.
With the destiny of each team tied to its performance and mother luck at this stage of the AFCON 2019 tournament, Super Eagles have started perfecting the act of penalty kicks in case the match on Saturday ends in deadlock.
The Super Eagles of Nigeria have qualified for the quarter-final of the ongoing Africa Cup of Nations in Egypt.