Ahmed Samir Farag opened the score line 15 minutes from time and Mohamed Abdul-Wahed sealed the victory with a stoppage-time strike.
The Dervishes went through with a 3-0 aggregate victory to continue their bid towards the first Confederation Cup title for any Egyptian team.
Ismaili's display was largely affected by the absence of Omar Gamal through suspension as they lacked rhythm in midfield.
The hosts could have gone ahead after just eight minutes when Wydad's defender Younes Manqari's misdirected header from an Ismaili cross went just wide of the Moroccan post.
In the 26th minute, Sayed Moawad's low cross from the left flank was brilliantly back-heeled by Mohamed Mohsen Abou-Greisha into the path of Abdullah Saied, whose first timer went over the bar.
Ismaili then dominated possession but couldn’t impose any threat on the visitors' net, failing to capitalize on Wydad's below-par form.
Saied narrowly failed to get on the end of Mohamed Fadl's neat chip that beat the offside trap 11 minutes after the interval.
Farag broke the deadlock in the 75th minute when a mis-hit clearance fell to him on the edge of the area before the former Sochaux playmaker sent a right-footed drive past Wydad keeper Hakim Mouzaki.
Seven minutes from time, a tamed left-footed shot from Kalilou Traore missed the target.
Abdul-Wahed added the second three minutes into stoppage time with an unstoppable bullet that went into the right top corner of the net from a tight angle.