Football’s world governing body FIFA had suspended the Sierra Leone Football Association in October due to “government interference”.
CAF’s decision means Kenya and Ghana are assured of first and second place in Sierra Leone’s Group F and have therefore booked their place in next year’s finals.
“Sierra Leone is disqualified from the qualifiers and all its matches are annulled,” CAF said in a statement.
The row stems from the decision of Sierra Leone’s anti-corruption commission to sack SLFA president Isha Johansen and general secretary Christopher Kamara during an ongoing probe into corruption and mismanagement.
In October, CAF cancelled two matches pitting Sierra Leone against Ghana due to the dispute between Freetown and FIFA.
The 2019 finals have been plunged into uncertainty after CAF last week stripped Cameroon of the right to host the tournament, citing delays caused by infrastructure work.
The organization has yet to determine the new host country but said it would reach a decision by the end of the year.