Despite enjoying the lion's share of possession in the first half, the Super Eagles struggled to break Lesotho's defence.
It needed a penalty for Nigeria to go ahead and captain William Troost-Ekong assumed the responsibility to convert from the spot 10 minutes into the second half.
Even after trailing, the hosts never showed any intention to hit back and it was actually the West Africans who nearly doubled their advantage on 62 minutes when Victor Osimhen was denied by the upright post.
Osimhen was back against to rattle the post from a tight angle with 12 minutes to go as Nigeria searched for a goal to cushion their lead.
Debutant and substitute Akor Adams' low shot then extended the Super Eagles' lead with 10 minutes to go.
But Likuena pulled back with seven minutes remaining when Hlompho Kalake graciously pounced on Stanley Nwabali's miscalculated punch in, to leave Nigeria at a risk of being levelled.
Some miscommunication between Sami Ajayi and Nwabali almost gifted Lesotho an equaliser, but Nigeria survived as an effort by the hosts went just wide.