Morocco were kicked out of the 2017 and 2019 Africa Cup of Nations Friday while Equatorial Guinea were punished for the unrest in Thursday's semi-finals in which 36 fans were injured.
Morocco were also fined $US1 million ($A1.28 million) and ordered to pay just over 8 million euros ($A11.76 million) in compensation after they refused to host this year's event due to fears over Ebola.
The Confederation of African Football (CAF) executive committee also announced that Equatorial Guinea, who stepped in to host the 2015 event, were being fined $US100,000 ($A128,000) after violent scenes in their 3-0 semi-final defeat to Ghana.
Meanwhile, Tunisia's soccer chief was banned from all African football activities for claiming his team was cheated out of a quarter-final win against the hosts.
CAF refused to accept Morocco's reasons for pulling out of hosting the 2015 event.
"The CAF executive committee considered that, contrary to what the Royal Moroccan Football Federation cited, force majeure cannot be accepted for the benefit of the federation," said CAF.
"CAF decided to suspend the national team of Morocco from the next two editions of the Africa Cup of Nations, 2017 and 2019, and to impose on the federation the regulatory fine of $1 million.
"...they decided by a separate measure to be borne by the Royal Moroccan Football Federation the sum of eight million and fifty thousand euros in compensation for all material damage sustained."
Despite disturbances blamed on Equatorial Guinea fans in Thursday's semi-final defeat to Ghana in Malabo, supporters will still be allowed into the country's third-place playoff against Democratic Republic of Congo on Saturday.
CAF meted out the fine to the Nations Cup hosts "for aggressive behaviour and being repeat offenders" for crowd trouble, said a confederation statement.
An order to play Saturday's third place playoff behind closed doors was suspended "to promote a spirit of Fair-play and brotherhood during the AFCON2015".
But CAF made it clear that if there was more unrest then it would "automatically impose the sanction of playing behind closed doors the Equatorial Guinean team's next official match".
Saturday's playoff is being held at the same 15,000-seater stadium in Malabo where Equatorial Guinea's supporters pelted Ghanaian fans with plastic bottles and chairs on Thursday night.
The game was halted for over half an hour with Ghana eventually winning 3-0 to set up a final on Sunday with Ivory Coast in Bata.
As the missiles rained down, the 500 visiting Ghana fans poured onto the pitch and play was halted eight minutes from time as security officials battled to regain control.
The Ghana Football Association (GFA) described the scene as a "war zone."
After the match, the Ghanaian supporters were kept at the stadium for several hours while further chaos ensued outside the ground.
Equatorial Guinea supporters broke street light poles and overturned vendors' tables.
The Ghana team were escorted to Malabo airport for the short flight from the island city to Bata on the mainland.
Equatorial Guinea's governing Democratic Party blamed the country's "eternal enemies" for Thursday's violence in Malabo.
It hit out at "the acts of provocation designed to create the disorder... perpetrated by the eternal enemies and detractors of our people and by their agents who wanted to disturb the peace".
Tunisia football chief Wadie Jary was banned from all CAF activities on Friday following claims his side were unfairly treated during their defeat to Equatorial Guinea.
CAF ordered Jary and the Tunisian federation to apologise or provide evidence to back up their complaints before midnight on Thursday.
However when no apology was forthcoming, CAF suspended Jary until an apology materialised.
Tunisia were warned they also face the same fate as Morocco and will be banned from the 2017 Cup of Nations if they fail by March 31 to supply either an apology or proof of bias.
Tunisian tempers flared after Mauritian referee Rajindraparsad Seechurn awarded the hosts a dubious stoppage-time penalty which resulted in the equaliser in their quarter-final clash.
When the final whistle sounded after Equatorial Guinea won 2-1, riot police had to protect the match officials from furious Tunisian players.
CAF banned Seechurn for six months and dropped him from the elite referees panel.
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