Second half strikes from Abdi Idleh Hamza and Mohamed Salem Breik was enough for Djibouti to record a 2-0 win over South Sudan at the Gouled Stadium in the capital, Djibouti.
Elsewhere at the Stade Nacional 12 de Julho in Sao Tome, an own goal by Jordao Diogo on 68 minutes handed visiting Madagascar victory at the expense of hosts Sao Tome and Principe in the encounter watched by a little over 2000 fans. The result marked a perfect start for new Madagascar coach, Frenchman Nicolas Dupuis, who was appointed few days to the encounter.
The second leg will take place in Antananarivo on Sunday.
Meanwhile, Comoros host Mauritius on Friday in Mitsamiouli with the return leg due four days later in Belle Vue.
The prelims involves the six least ranked teams on the continent, which will see the three winners joining the 45 others for the group phase.
22.03.2017 Sao Tome Sao Tome 0-1 Madagascar
22.03.2017 Djibouti Djibouti 2-0 South Sudan
24.03.2017 Mitsamiouli Comoros vs Mauritius