Morocco was also banned from the next two tournaments in 2017 and 2019, Africa's football body announced.
In addition to the fine, CAF said it was seeking around $9 million in compensation from the North African nation for backing out of the hosting agreement.
Morocco Football Federation vice-president Nourreddine El Bouchhati told a local news website that "a meeting will be held within the federation to discuss the measures to take."
CAF said the decisions were made by its executive committee, which met in the Equatorial Guinea capital of Malabo during the ongoing African Cup.
Equatorial Guinea stepped in at short notice late last year to host the three-week tournament in Morocco's place. It ends on Sunday.
Morocco had declined to stage the 16-team championship on its scheduled dates of Jan. 17-Feb. 8, citing fears over the spread of Ebola from West Africa. It asked CAF for a delay. CAF refused and approached Equatorial Guinea.
CAF said in Friday's statement that it considered Morocco's request that the tournament be delayed until October a "refusal" to host. CAF rejected Morocco's stance that it needed to postpone the tournament because of high health risks from fans travelling from Ebola-affected regions in West Africa.
The deadly Ebola virus has killed nearly 9,000 people in the outbreak, mainly in the three worst-affected countries of Liberia, Sierra Leone and Guinea. Only Guinea qualified for the final tournament.
The $9 million in damages demanded by CAF is "in compensation for all material damage sustained by CAF, stakeholders and partners as a result of the decision (by Morocco) not to host AFCON 2015," CAF said.
Moroccan soccer authorities had been expecting a financial penalty but no tournament ban, and the severity of the punishment appeared to have taken them by surprise.
Last month, federation president Faouzi Lakjaa told a local radio station that there would be "no sports sanction," and Morocco and CAF were moving toward an arrangement to settle the final bill.
He reiterated that stance on Thursday, a day before CAF's announcement.
The sanctions will put more pressure on the extremely strained relationship between North African countries and CAF, which has been led for nearly 30 years by Cameroon's Issa Hayatou.
Earlier Friday, CAF suspended Tunisia's federation president and threatened that country with a ban from the 2017 African Cup if it didn't apologize for suggesting the body was biased against it. Tunisia refused to apologize.
Associated Press writer Paul Schemm contributed from Rabat, Morocco.