A 2-1 defeat to Tunisia dashed the hopes of the tournament's most successful side while Mali booked their placePrevious champions Egypt failed to reach the Africa Cup of Nations as qualification drew to a close on Wednesday.
Egypt's chances of securing the qualifying spot for the best third-placed team were dashed when they surrendered a lead to lose 2-1 at Group G winners Tunisia.
With Tunisia and Senegal having already qualified, Egypt - the most successful team in Afcon history - needed to win by at least two clear goals to earn a reprieve but fell short.
Senegal rounded off their campaign with a 3-0 win at home to Botswana.
Egypt's failure meant that Democratic Republic of Congo take the vacant spot for the best of the rest after they defeated Sierra Leone 3-1 in Group D.
In Group B Mali's 2-0 win over table-toppers Algeria saw them progress at the expense of Malawi who could only draw 0-0 with Ethiopia, while in Group C Gabon overtook Lesotho courtesy of a 4-2 win and Burkina Faso ended their successful campaign with a 1-1 draw against Angola, going through top.
Elsewhere, Cape Verde lost 1-0 at Zambia but both teams had qualified from Group F. The pool's other sides Niger and Mozambique drew 1-1.