DR Congo could only draw 1-1 with their rivals in Kinshasa, having drawn the first leg of their qualifier 0-0.
It put Congo Brazzaville through on the away-goals ruling.
Also on Saturday, Zambia knocked out South Africa with a 2-0 win in Ndola to progress 4-2 on aggregate.
|African Nations Championship qualifiers - first leg scores in brackets|
|Aggregate winners qualify for finals in Kenya from 11 January to 2 February|
|Friday:||Ivory Coast v Niger (1-2)|
|Libya 1-1 Algeria (Libya win 3-2 on aggregate)||Mali v Mauritania (2-2)|
|Morocco 3-1 Egypt (Morocco win 4-2 on aggregate)||Sudan v Ethiopia (1-1)|
|Saturday:||Nigeria 2-0 Benin (Nigeria win 2-1 on aggregate)|
|Zambia 2-0 South Africa (Zambia win 4-2 on aggregate)||Sunday:|
|Rwanda 2-0 Uganda (Uganda win 3-2 on aggregate)||Namibia v Comoros (1-2)|
|DR Congo (holders) 1-1 Congo (Congo win on away goals)||Ghana v Burkina Faso (2-2)|
|Cameroon 2-0 Sao Tome e Principe (Cameroon win 4-0 on aggregate)||Tuesday:|
|Angola v Madagascar (0-0)||Guinea v Senegal (1-3)|
In other results on Saturday, Uganda progressed 3-2 overall despite a 2-0 defeat in Rwanda, and Nigeria overturned a 1-0 first leg deficit against Benin to qualify 2-1 overall thanks to a 2-0 win at home in their second leg.
On Friday, Morocco and Libya knocked out Egypt and Algeria respectively as they booked their places at Kenya 2018.
Morocco beat Egypt 3-1 in Rabat on Friday to win the tie 4-2 overall.
Libya held Algeria to a 1-1 draw in Sfax to go through to the finals with a 3-2 aggregate victory.
In Sunday's qualifiers, Namibia host Comoros looking to come back from a shock 2-1 defeat away from home.
Also, twice runners-up Ghana will aim to reach the finals for the fourth time in five attempts by overcoming Burkina Faso in Kumasi.
Ghana led twice in the first leg only for Iliase Sawadogo to snatch a 2-2 draw five minutes from time.
Despite CHAN matches only featuring locally-based footballers the games have full international status and count toward the monthly Fifa rankings.