Jordan Ayew gave the Black Stars a 42nd-minute lead from the penalty spot before Mubarak Wakaso doubled their lead at the end of the first half.
But trouble broke out as Avram Grant's team had to be shielded by police from objects thrown from the crowd as they left the field.
The home players pleaded for calm in the stands before the resumption but they were unable to negotiate a way back into the match as Andre Ayew sealed victory and a final spot against Ivory Coast with his third goal of the tournament.
Chaos then descended as the game entered its closing stages, with the game suspended for half an hour as a hail of objects were thrown by Equatorial Guinea fans into the visiting support.
Ghana supporters gathered on the running track behind one of the goals as they attempted to escape the missiles, while police used a helictoper and tear gas to disperse the offending fans.
The game eventually resumed with the clock set at 90 minutes and the Black Stars duly saw out the contest to reach the final where they will meet the Ivory Coast.
