Belsalam Al-Saied scored the winner in the 75th minute when he brilliantly headed home a corner kick, to give the visitors a substantial advantage in the continental competition.
Kabylie are now on top of Group B with three points. Ahli and Heartland have one point each after playing out a tame 1-1 draw earlier on the same day.
Ismaili are languishing at the bottom of the group with no points.
The Dervishes' lost in their first competitive game under the guidance of Dutch coach Mark Wotte, who has recently been reinstated at the coastal club.
Ismaili got the upper hand most of the game and carved out a number of clear-cut chances, could not find the net though.
They first came close to scoring with a powerful shot from Shadi Mohamed that was deflected off the Algerian defense and out of the pitch.
Ahmed Samir also tried his luck after 25 minutes but his fierce drive was blocked by the keeper.
Four minutes from halftime, Ahmed Ali connected with an Ahmed Sedik cross only to see his header go inches past the post.
Shams Al-Din Nasaakh could have put Algeria ahead when his low shot missed the target from close range.
Kabylie relatively redeemed themselves after the break but Ismaili remained in charge.
Samir fired another shot seven minutes from time but again missed the target.
Ahmed Ali also spurned a golden chance to put Ismaili ahead when he went one-on-one with the keeper, who easily saved the striker's chipped effort.
Kabylie defended tightly in the last 15 minutes of the game to maintain their lead till the final whistle.