The country's football federation has also been fined $1 million and ordered to pay $9.1 million "for damages caused to the Confederation of African Football (CAF) and partners."
Its officials had called for the tournament to be delayed as concerns over the potential spread of the virus grew, and then declined to host it when that delay was not granted.
That led to the CAF banning it from taking part in the 2015 event
after Equatorial Guinea had stepped in as host nation -- and African football's governing body has now imposed further, sweeping sanctions.
In November, only two months before the tournament was due to be played, Morocco's Sports Minister Mohamed Ouzzine informed CAF that the North African country would continue to ask for a postponement of at least six months.
Although there had been no diagnosed case of Ebola in Morocco, officials said the call for a postponement was "dictated by health reasons of the most dangerous kind, linked to the serious risk of the spread of the deadly Ebola pandemic."
The government believed thousands of traveling fans from West Africa posed a potential health hazard, although CAF countered by saying it believed less than 1,000 would travel from that region worst affected by the illness.
In a statement
, the CAF executive committee said it "took action on the refusal of Morocco to host this competition as scheduled and agreed."
The statement added: "Morocco had based its request to postpone the tournament on allegations "of the highest health risk."
Morocco cited the outbreak of the Ebola virus as a case of force majeure in justifying its request for postponement, citing in particular the risk of contamination of its population because of anticipated fans' flows.
"The executive committee considered that, contrary to what the Royal Moroccan Football Federation cited, force majeure cannot be accepted for the benefit of the federation."
Meanwhile, the CAF has fined Equatorial Guinea $100,000 (£65,000) after crowd trouble
marred Thursday's Cup of Nations semifinal defeat to Ghana.
The governing body also imposed a suspended punishment, ruling that the tournament hosts would have to play a match behind closed doors if there was any repeat of the problems at this weekend's third-place playoff against DR Congo.
It said Equatorial Guinea must pay for the treatment of the 36 fans injured in the clashes, which broke out during the closing stages of Ghana's 3-0 win at the Estadio de Malabo in Equatorial Guinea.
Officials stopped the game after 82 minutes, with Ghana fans having gathered behind one goal as they attempted to get away from missiles being hurled by Equatorial Guinea supporters.
With Ghana leading 3-0 through goals from Jordan Ayew, Wakasu Mubarak and Andre Ayew, the players were told to stand in the middle of the pitch as they awaited a decision on whether the game could continue.
A police helicopter hovered over the stadium before it was eventually decided that the match would be completed, and Ghana went on to seal their place in Sunday's final against Ivory Coast.
Trouble had threatened to boil over earlier on, with missiles thrown at Ghana players as they headed down the tunnel at half-time and the atmosphere in the stands souring as several decisions went against the home team.
said its disciplinary panel had imposed the fine for "aggressive behavior and being repeat offenders" after supporters had thrown missiles at Tunisia players following Equatorial Guinea's dramatic victory in the AFCON last eight.
"At least 36 people injured were identified by the medical teams present at the stadium following the incidents that marred the game," the statement said.
"All the injured were supported and attended to on site. A total of 14 were transferred to hospital units for further investigations, with one case requiring close monitoring."