Jane Thaba-Ntso scored an 84th minute winner to seal a 1-0 win for Lesotho over Group B rivals Malawi at the Sam Nujoma Stadium in Windhoek on Thursday evening.
Likuena will now face South Africa in the 2016 Cosafa Castle Cup quarterfinals on Saturday.
Malawi had to beat the mountainous nation to seal their place in the knockout stages, and stated their intent from the onset with Gerald Phiri Jnr forcing Daniel Jousse into two top-class saves within the opening exchanges.
Lesotho, though, were not content on sitting back and after Tsepo Seturumane skipped past his marker the Likuena striker should have done better with his resulting effort on the half-hour mark.
Bidvest bound Gabadinho Frank Mhango had a couple of chances to put the Flames in front either side of the break. On both occasions the forward was unable to hit the target as frustration within the Flames camp mounted.
Having survived a sustained spell of pressure, Lesotho provided the sucker punch against the run of play.
Thabo-Ntso providing the finishing touches to a pin-point cross by Thabo Seakhoa with six minutes remaining.
Malawi (0) 0
Lesotho (0) 1 (Thaba-Ntso 84')
Malawi: Swini; Sanudi, Gabeya, Nyirenda, Mlimbika - Gerald Phiri (Wadabwa 76') Jnr, Kaliati (Banda 61'), Namwera, Kamwendo - Mhango, Msowoya (Sulumba 41')
Lesotho: Jousse; Moremoholo,Makepe,Tseka,Kamela - Khutlang (Seakhoa 57'), Kalake, Mahula, Thaba-Ntso - Seturumane (Motebang 54'), Potloane (Mkhwanazi 77')