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The score would have been significantly more one-sided had Morocco taken all their chances as they overwhelmed the tournament debutants at the Ahmadou Ahidjo Stadium.
Amallah opened the scoring by blasting home from close range after picking up a rebound following some frenetic defending to give Morocco a deserved lead.
Morocco picked up the pace in the second half and at times laid siege to the goal but found Comoros goalkeeper Salim Ben Boina hard to beat, while also missing some glaring chances.
El Kaabi was again guilty of wasting opportunities while the Comoros defenders tackled desperately to keep their star-studded opponents at bay.
En-Nesyri, whose participation at the tournament had been in doubt because of injury with his Spanish club Sevilla, came on in the second half for his first run out in a boost for Morocco but had his spot kick saved.
But former Dutch youth international Aboukhlal finally doubled the lead for Morocco as he tucked away a goal in the last minute. He was initially flagged offside but the decision overturned after consultation with VAR.