Avram Grant's side eased into a 3-0 lead thanks to goals from Ayew brothers Jordan and Andre as well as a strike from Mubarak Wakaso.
However, disturbances from the stands were a constant throughout as the Equatorial Guinea players were outclassed on the pitch.
Bottles were thrown at the Ghana bench and towards the pitch while Grant, his staff and his players had to be escorted off the pitch at half-time by riot police.
The Ghana fans were eventually targeted in the second half, a large group of fans running from the stands and taking to safety at the edge of the pitch - a running track between them and the stands keeping them out of reach.
That caused play to be stopped in the 84th minute and, as the home players repeatedly asked the offenders for calm and a police helicopter even emerged at the scene, the match was delayed by over half an hour with Gabonese referee Eric Arnaud Otogo-Castane seemingly unwilling to abandon play.
The Ghana Football Association were heavily critical of the situation while covering the game through their official Twitter account.
One post read: "Police helicopter hovers above the pitch with the #Ghana fans in real danger. It's now like a war zone."
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