The host nation upset the odds by making fairytale progress to the semi-finals but the dream turned sour in Malabo on Thursday night.
A 42nd-minute penalty from Jordan Ayew and further goals by Mubarak Wakaso and Andre Ayew ensured routine passage to Sunday's final against Ivory Coast for Avram Grant's team.
But the Ghana players were shielded by police from objects thrown from the crowd when they left the field at half-time and the situation in the stands deteriorated during the second half.
During the closing stages of the match, referee Eric Arnaud Otogo-Castane halted play as Ghana fans targeted by missiles from the home fans sought refuge behind one of the goal.
The players remained on the field amid much confusion during a delay that lasted more than half an hour before Otogo-Castane resumed the action, playing out a nominal period of stoppage time to bring the game to a close.
"I've never played in front of anything like that," Nsue told reporters after the match.
"I'd like to say sorry on behalf of my team. It was an odd experience – one I've never felt before.
"Ghana played very well."
Equatorial Guinea are scheduled to meet Democratic Republic of Congo in Saturday's third-place play-off.
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