The home-based Black Stars held their own to keep the Stallions from scoring in the final round second leg fixture in Ouagadougou.
The result meant the Black Stars B got eliminated 1-0 on aggregate after suffering defeat at home in the first leg tie at the Baba Yara Stadium.
The Local Black Stars beat the Stallions 4-1 on penalties two weeks ago en route to reaching the final of the 2019 WAFU Cup of Nations in Senegal.
But Maxwell Konadu and his charges could not replicate that feat and got knocked out of the competition.
It is the second time in a row coach Maxwell Konadu's outfit are denied a place at Chan by Burkina Faso following a similar situation in the 2018 tournament qualifiers in 2017.