The win left Pyramids top of the group with 10 points from four matches, three points clear of second-placed Berkane.
Zambia’s Power Dynamos are third on four points after a 1-0 away win over bottom side Rivers United of Nigeria, who have one point.
Pyramids need just one point from their remaining two group matches to secure a place in the last eight.
Mahmoud Abdel-Hafiz, known as “Zalaka”, gave the hosts an early lead in the 11th minute, heading home Nasser Maher’s cross.
Berkane pushed for an equaliser but were unable to break down the Egyptian side’s defence.
Maher then turned scorer in the 74th minute, netting his first goal for Pyramids since joining from Zamalek in the January transfer window. Ahmed Atef added a third six minutes later to seal a comprehensive win.
Defending champions Pyramids next travel to face Rivers United on Sunday.
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