Bushy Moletsane's goal midway through the second half was enough to give Lesotho a narrow 1-0 home victory over Kenya in Maseru.
The return leg of their second qualifying round tie takes place in Nairobi in two weeks' time and Lesotho will be wary of Kenya's strong home record, which has seen them go over a year - and seven games - unbeaten on home soil.
Congo, though, can be more confident of reaching the Cup of Nations finals after they beat Rwanda 2-0 in Point-Noire, courtesy of late goals from Cesaire Gandze and Ferebory Dore.
Benin have captain Stephane Sessegnon to thank for their 1-0 home win over Malawi as the West Brom star scored the only goal of the game after 19 minutes.
And in Sunday's other qualifying clash, Mozambique left it late to snatch a 2-2 draw in their first leg in Tanzania.
Domingues had given Mozambique the lead with a penalty three minutes after half-time, only for Tanzania's Khamis to turn the game on its head with a quick-fire double.
However, Isac had the final say, scoring in the 89th minute to ensure Mozambique will begin their home leg in Maputo on level terms.