The East African giants have dropped by a place and are now ranked 84th worldwide.
The Cranes would have progressed had they picked a point in the last group qualifier against Malawi.
However, after drawing against Burkina Faso 0-0 at St Mary’s Stadium at Kitende, they went down 1-0 to The Flames in Blantyre.
This ended any hope of Cranes going to the finals.
Despite the draw and progress to the Afcon finals, Burkina Faso dropped by two places.
They are now ranked in 60th position globally.
Malawi, who booked a third Afcon slot in their history, moved eight places up and are now in position 115.
Sudan, who stunned South Africa to join the Cameroon party, moved four places up and are now ranked 123rd.
Rwanda, another Eastern African nation that failed to qualify for the Afcon finals have moved four places up and are now 129th in the global register.
Burundi dropped by two positions and the latest rankings placed them at 142nd.
South Sudan – whose push for a maiden Afcon slot failed – dropped by six places and they are now ranked in position 169th globally.
The horn of Africa nation Djibouti saw their position improve by one place and are 183rd.
Sao Tome and Principe, Somalia, Seychelles and Eritrea are the four bottomed placed CAF nations as they are 190, 197, 200 and 203 respectively.