Sierra Leone's fate was decided by the Confederation of African Football (CAF) on Monday after the nation was suspended by FIFA over government interference in football in October.
That meant that the Leone Stars were unable to fulfil their last three qualification matches, and have now officially been withdrawn from the preliminaries by CAF and their previous two results annulled.
Kenya, who will make a first Nations Cup finals appearance since 2004, head the revised three-team qualification pool with seven points, followed by Ghana who are a single point behind.
With the top two sides advancing to the expanded 24-team finals, Ethiopia are a distant third with a one point from four games and no more fixtures to play.
FIFA's decision to ban Sierra Leone came after it wrote to the African country's sports minister expressing "grave concern" about the removal of SLFA president Isha Johansen and general secretary Christopher Kamara.
The Anti-Corruption Commission in the country had followed through on a threat to raid the SLFA amid allegations of match-fixing involving the national team, and barred Johansen and Kamara from the offices.
FIFA are also looking at matches as far back as a World Cup qualifier against South Africa in 2008 as part of their own investigation into the match-fixing allegations.
Both Johansen and Kamara deny any wrongdoing.
The host nation for the Nations Cup next year will be decided by Dec. 31 after CAF stripped Cameroon of the tournament after concerns over the slow pace of preparations.
Morocco and South Africa are the likely replacements for what will be the fourth successive Nations Cup to have a change of host.
(Reporting By Nick Said; Editing by Christian Radnedge)
