But it was a far from convincing passage to the knockout stage by the home nation with success coming via an own goal four minutes from time in Brazzaville.
The Congolese had been on the back foot at Stade de l'Unite for some time before they forced a corner from which Fousseni Beao headed into his own net.
Success coupled with Sudan and Zimbabwe drawing 0-0 at the same time in another Brazzaville stadium ensured the hosts of a top-two finish.
Congo have six points in Group A, Burkina Faso three and Sudan and Zimbabwe one each going into the final round of mini-league fixtures.
If the Burkinabe avoid defeat against the Sudanese Sunday they will join the Congolese in the semi-finals of the under-23 tournament.
Junior Makiesse put Congo ahead after four minutes against Burkina Faso by controlling an overhit cross, drifting across two defenders and beating goalkeeper Kouakou Koffi with a deflected shot.
Ziem Somda levelled on 62 minutes as his free-kick from near the touchline looped over giant goalkeeper Christoffer Mafoumbi and into the net off the underside of the crossbar.
The goal galvanised the Burkinabe into seeking a winner and they looked likelier to score until Beao blundered under pressure from Congo captain Sagesse Babele.
Nigeria advanced to the semi-finals Wednesday with a convincing 2-0 Group B victory over arch-rivals Ghana through goals from Junior Ajayi and Kingsley Sokari.
Senegal or Ghana will join them after the withdrawal of Egypt -- who did not want to compete with a severely depleted squad -- reduced the mini-league to three teams.