Alexander Djiku scrambled the ball into the net at the back post from a Jordan Ayew corner to seal a crucial three points for his nation.
Ghana now lead the table with 19 points, three ahead of second-placed Madagascar and four more than Comoros. The Black Stars travel to Central African Republic and host Comoros in their final two qualifiers next month.
Madagascar kept their qualifying hopes alive with a 3-1 home win over Chad, having trailed at half-time. Goals from Caddy Warren, Rayan Raveloson and Hakim Abdallah sealed the win.
Morocco won 2-0 in Zambia in Group E as Youssef En Nesyri and Hamza Igamane scored to keep up their momentum.
Algeria held
Algeria were held to a 0-0 draw by Guinea and now only have a four-point lead in Group G over Uganda and Mozambique, who both won 2-0 on Monday.
Mozambique beat Botswana thanks to goals from Witi and Faisal Banga, while Uganda's Allan Okello with a penalty and Jude Ssemugabi scored in their victory over Somalia.
Libya's Muad Eisay and Ezoo El Mariamy were on target in the first half in their side's 2-0 victory over Eswatini in Group D.
Libya are in third in the pool with 14 points, one behind Cameroon and two off leaders Cape Verde, who both have a game in hand and meet on Wednesday.
The nine group winners qualify for the World Cup in North America with the four best runners-up going into the playoffs in November to battle for one further place at the finals.