The Kenyan minnows, who were eliminated by the Egyptians last year, go through with an aggregate 4-2 victory.
The Dervishes were hampered by the injury of influential skipper Hosni Abd-Rabou early on as the Egypt midfielder made way for Abdullah Saied before the break.
To make matters worse for the visitors, another international was forced off at half time, with Amr Al-Sulaya replaced by Mohamed Hommos.
An 11-minute blitz saw the home side take charge of the tie by scoring three goals in the last half hour.
Congolese striker Bob Mugalia scored a quickfire brace on 26 and 33 minutes, shortly before Titus Mulama netted the all-important goal to put Sofapaka in front.
Ismaili committed men forward and almost snatched the vital away goal, only to concede a fourth in injury time, thanks to a strike from Patrick Kagogo.