With the knowledge that only a win would brighten their chances of making it to the quarter-finals, Basem Morsi handed the Egyptians a positive start after he got the curtain raiser in the 14th minute.
On the stroke of halftime, Talaat Youssef’s men responded with the equaliser. Mahmoud Hamdi was sent off for a second caution for a foul in the penalty area, and Anis Saltou stepped up to dispatch the resulting spot-kick past Ahmed El Shenawy.
In the 69th minute - three minutes after Nigerian striker Stanley Ohawuchi was introduced, the Boss made their numerical advantage count as Vianney Mabide handed them the lead for the first time in the encounter.
With a quarter of an hour left, Youssef made it 2-2 for Augusto Inácio’s side but it was not enough to see them through as the Libyans stood firm to deny their hosts a victory to secure a passage to the next round of the Caf Champions League.
The former Kwara United versatile player will not be able to add to his first strike in Africa's premier competition as the result saw Zamalek finished third in Group B with six points.
While USM Algiers, after handing a 4-1 defeat to bottom-placed Zimbabwean outfit, CAPS United stay atop with 11 points and Al Ahli claimed second spot with nine points.