Issa latched onto a fine threaded pass from veteran playmaker Abdallah El-Said to break clear and score from close range.
Despite the win, the Egyptian side remain second in their group with 13 points, on level with leaders Ahly Tripoli as both sides advanced to the knockout stage.
The Libyan side topped the group due to their better head to head record over Pyramids.
They lost 2-1 to Pyramids in Cairo before claiming a 1-0 win at home.
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