Ghana progressed to Sunday's final with a 3-0 win in Malabo on Thursday, but crowd trouble forced a lengthy suspension in play before the last-four match could be completed.
Projectiles were aimed at Ghana officials and fans, who were forced onto the pitch in search of safety, with governing body CAF revealing 36 people were injured and 14 taken to hospital.
Kwesi Nyantakyi, the president of the Ghana Football Association, subsequently suggested lives could have been lost in the incident, but CAF has acted quickly to issue sanctions.
The hosts will cover the treatment costs of all of those injured at the fixture, while the country's football federation has been fined $100,000 for "aggressive behaviour" and being repeat offenders.
Equatorial Guinea have also been ordered to play a match behind closed doors, although this is suspended for the third-place play-off and will only come into effect in the event of a repeat occurrence on Saturday.
The federation has already had to pay a $5,000 for the behaviour of the country's fans in the quarter-final match between Tunisia and Equatorial Guinea.
Watch every match of the Africa Cup of Nations LIVE on British Eurosport HD or sign up to Eurosport Player and follow the action on mobile, tablet and other devices: www.eurosportplayer.com
