Pierre-Emerick Aubameyang failed to guide Gabon to the 2019 Africa Cup of Nations in an encounter that saw Saido Berahino help Burundi seal their maiden ticket for the continental showpiece.
The Swallows settled for a 1-1 draw in their final Group C qualifying match to make history on Saturday.
With Burundi just in need of a draw to secure their place in Egypt, Cedric Amissi opened the scoring at the Prince Louis Rwagasore Stadium in the 76th minute but Omar Ngando's own goal was not enough for Gabon who needed a win to qualify.
Aubameyang was on parade for the entire duration of the match but could not help Daniel Cousin's side get much needed points in Bujumbura.
The 2017 Afcon hosts ended the qualifiers in the third place with five points from six matches while Burundi finished second with 10 points from six games.