Nigeria fell from the 6th position it held the FIFA rankings for Africa to 8th dropping two places for Zambia and Libya who moved to 6th and 7th respectively.
Globally, the Super Eagles plummet from 45 to 56th on the rankings.
Zambia shot up 28 places in the FIFA rankings, breaking into the top 50 for the first time in eleven years after winning the African Nations Cup on Sunday.
The Chipolopolo (The Copper Bullets) moved into 43rd spot, their highest position since February 2001, after beating Ivory Coast on penalties following a goalless final in Libreville.
Despite losing the decider, Ivory Coast climbed three places to 15th and are the continent's highest-placed team. The Elephants did not concede a goal in the tournament.
Mali, who finished third, moved up 25 places to 44th, one ahead of co-hosts Gabon, who leapt 46 places after reaching the quarter-finals with wins over Niger and Morocco.
Fellow co-hosts Equatorial Guinea, a team made up largely of Spanish lower league players, leapt from 151st to 110th after surpassing all expectations by reaching the quarter-finals.
Spain stayed top of the rankings while Germany moved up to second and Netherlands dropped to third even though neither side played a game in the last month.
FIFA said the change was "due to the devaluation of matches from previous years."
Similarly, Brazil dropped to seventh and Portugal moved up to sixth while Argentina dropped out of the top ten, losing their place to Denmark.