Lesotho had not claimed a qualifying win for seven years, but overturned a 1-0 first-leg deficit to book a tie with Kenya.
Mabuti Potloane put Lesotho in front on Sunday and a Sekou Oliseh own goal on the stroke of half-time proved decisive.
Congo and Equatorial Guinea also recovered from first-leg deficits to progress to the second round.
A goal behind from the first leg, Congo were made to wait until the stroke of half-time for Silvere Ganvoula to level the tie.
Fode Dore and Ladislas Douniama then added further goals to ensure Congo made it through to the next round, where they will face Rwanda.
Equatorial Guinea trailed in their qualifier against Mauritania but found three goals in Malabo to book a second-round meeting with Uganda.
While Tanzania may have had a one-goal lead to rest on from their first leg, they were given a stern test by Zimbabwe in Harare as the hosts drew level just three minutes in.
Tanzania recovered to claim a 2-2 draw and run out 3-2 winners on aggregate.
Botswana were made to sweat by Burundi following a goalless first leg, but Joel Mogorosi scored to send his nation through to a meeting with Guinea-Bissau.
Benin enjoyed a much smoother progression as Stephane Sessegnon scored on his birthday to help secure a 4-0 aggregate win over Sao Tome e Principe.
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