Democratic Republic of Congo beat Sierra Leone 3-1 at home, hosts Cameroon secured a 2-0 result over Namibia and Ivory Cost overcame Gambia 2-1.
Senegal, who are awaiting a court decision on their status as Africa champions, posted a 4-1 triumph over Sudan in new coach Patrick Vieira's home debut.
Ghana lost their opening two Group C games in a shock setback at the start of the 2027 qualifying campaign and fired veteran coach Carlos Queiroz, putting women's team coach Kim-Lars Bjorkegren temporarily in charge.
Captain Jordan Ayew had his 14th-minute penalty saved as 200th-ranked Somalia proved stubborn opposition, but Jonas Adjetey's header in first-half stoppage time put the home side ahead and Felix Afena-Gyna added a second soon after the break.
DR Congo, who like Ghana reached the second round at this year's World Cup, moved closer to securing early qualification as they won a third successive Group E game.
Yoane Wissa' fourth-minute goal set the platform, and Samuel Moutoussamy made it 2-0 in the 35th minute with a superb right-footed strike into the top corner before midfielder Edo Kayembe added a third early in the second half.
The Congolese, with three qualifiers left, are five points clear of Equatorial Guinea and Zimbabwe, who played out a goalless draw.
Senegal were being held 1-1 at halftime by Sudan after Nicolas Jackson opened the scoring, but Mohamed Abuaagla equalised.
Boulaye Dia, Ibrahim Mbaye and debutant Pathe Mboup scored in the second half to ensure Senegal top Group J.
Cameroon fielded a youthful side with 27-year-old captain Bryan Mbeumo the oldest player but were still too strong for Namibia as Saidou Alioum and Bil Nsongo scored in the first half hour in Douala.
Ivory Coast struggled at home to tiny Gambia, who had upset Ghana 4-2 away in their last game in September.
Malick Yalcouye and Elye Wahi put Ivory Coast ahead in Bouake, but Musa Barrow pulled one back to ensure an uncomfortable finish for the hosts.
Benin trounced the Central African Republic 4-1 in Group F with a double from Aiyegun Tosin, while Guinea beat Eritrea 2-1 in Group D.
The finals are being co-hosted by Kenya, Tanzania and Uganda from June 19-July 17 next year.
