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.