Mohammed Kudus scored both goals for Ghana but the “Black Stars” defensive mistakes allowed Omar Marmoush and Mostafa Mohamed to level the score twice.
With the draw, Egypt sit in second place with two points, trailing group leaders Cape Verde by one point.
Cape Verde will face Mozambique on Friday. Ghana remains at the bottom of Group B with just one point, level with Mozambique.
The match did not start well for the Pharaohs, and they suffered a setback just before halftime when Liverpool ace Mohamed Salah was forced off the field due to a left thigh injury.
However, Ghana was boosted by the return of Mohammed Kudus, who had recovered from a hamstring injury.
He scored in first-half injury time, shortly after Salah’s departure, with a powerful shot from outside the area.
Kudus had another chance in the second half, but Egypt had a goal from Mohamed Abdel-Moneam disallowed for offside after a VAR review.
Marmoush then equalized in the 69th minute after capitalizing on a backpass mistake from Iñaki Williams.
However, Kudus quickly responded, with a shot that took a slight deflection off Abdel-Moneam and found the back of the net.