Ethiopia continued their sudden revival over the last month as they drew away in Benin to advance on the away goals rule while the Congolese had a routine win over the Seychelles, Africa's smallest nation.
Also advancing after Sunday's matches were Mozambique, Togo and Zimbabwe.
Ethiopia, who have made an impressive start to World Cup qualifying over the last fortnight, were again successful in the Nations Cup as Adnane Girma scored the decisive away goal in Cotonou. The 1-1 draw on Sunday followed a goalless tie in Addis Ababa in February in the first leg.
Congo beat the Seychelles 3-0 in Kinshasa with goals from Dieumerci Mbokani,Issama Mpeka and Deo Kanda. They progress 7-0 on aggregate.
German-based striker Knowledge Musona scored a 36th minute to give 10-man Zimbabwe a narrow 1-0 home triumph over Burundi and advance on the away goals rule. They had lost February's first leg away 2-1.
Togo won in the same fashion over Kenya in Lome thanks to Serge Gakpe's second half winner.
Mozambique eliminated Tanzania in a dramatic post-tie penalty shootout after they ended 2-2 on aggregate. Mozambique won 8-7 on penalties in Maputo.
Progressing earlier on the weekend were former champions Algeria, Cameroon, Nigeria.
The 14 winners of the first round ties go to the final round where they will be paired against the 16 teams who competed at the 2012 Nations Cup, also to be played over two legs later this year. The draw is scheduled for July 5.