The match in Cape Coast was a dead rubber as the 'Pharaohs' won the mini-league and secured a place at the 2018 finals in Russia by defeating Congo Brazzaville last month.
Argentina-born Egypt coach Hector Cuper rested a number of first choices, including Liverpool forward Mohamed Salah, giving fringe players like Shikabala a chance to impress.
The Saudi Arabia-based midfielder made the most of his first national team appearance for three years by slamming a low pass past goalkeeper Richard Ofori on 61 minutes.
But the lead lasted only three minutes with Ghana levelling through an Edwin Gyasi shot from outside the box that took a deflection and wrongfooted goalkeeper Sherif Ekramy.
The 'Black Stars' almost snatched victory in the fourth and final minute of stoppage time during a goalmouth scramble.
Ghana lacked several regulars, including Andre and Jordan Ayew, Asamoah Gyan and Thomas Partey.
Congo and Uganda drew 1-1 in Brazzaville with Marvin Baudry giving the home team an early lead that was cancelled just one minute later by Milton Karisa.
Egypt topped the final standings with 13 points followed by Uganda (nine), Ghana (seven) and Congo (two).