The game was a dead-rubber affair as The Pharaohs had already clinched the group’s sole ticket.
After a goalless first half, Shikabala gave Egypt the lead in the 61st minute, firing an unstoppable left-foot shot which flew past Richard Ofori in goal for Ghana.
But just three minutes later Edwin Gyasi equalised for Ghana with a left-foot strike which took a slight deflection.
Egypt finished the qualifiers on 13 points with Ghana in third spot on seven points.
In the other game in the group also played on Sunday, Congo were held to a 1-1 draw by Uganda.
Uganda were second behind Egypt on nine points and Congo bottom with just two points.