The host nation were dumped out of the tournament in shame when crowd trouble marred Ghana's 3-0 semi-final victory in Malabo on Thursday.
Play was suspended for a lengthy period as projectiles were aimed at Ghana officials and fans, who took shelter behind one of the goals amid unsavoury scenes.
The Confederation of African Football (CAF) revealed 36 people were injured - with 14 taken to hospital - as Ghana's progress to the final was overshadowed by violence.
CAF on Friday fined the Equatorial Guinean Federation $100,000 and ruled that it must pay treatment costs for fans that were injured.
Equatorial Guinea will also play one game behind closed, but only if there are more problems in Saturday's third-place play-off.
Only five days earlier there were jubilant scenes in Bata, where Javier Balboa inspired a dramatic fightback from the hosts to take them from the brink of going out of the tournament to the semi-final.
Balboa scored a controversial stoppage-time penalty to take the tie against Tunisia into extra time, and became even more of a hero as he netted a sublime free-kick to secure a 2-1 victory.
That win put the hosts into their first AFCON semi-final and it is unfortunate that off-field events have hit the headlines, rather than the achievements of Esteban Becker's side.
Becker, who only took over as coach 11 days before the tournament started, must now try and pick his side up after the events on Thursday, but the Argentine has exceeded expectations regardless of the outcome.
Equatorial Guinea, ranked 118th in the world, only entered the tournament in November when they replaced Morocco as hosts because of the Ebola crisis and they will be eager to sign off in style this weekend.
DR Congo's hopes of being crowned African champions for the first time since 1974 were ended when they lost 3-1 to Ivory Coast on Wednesday.
Florent Ibenge's men can also hold their heads up high following their exploits in the tournament, with an incredible 4-2 quarter-final win over neighbours Congo the highlight.
DR Congo came back from two goals down with just over an hour played to reach the last four and will be eyeing third place for the first time in 17 years.
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