Lesotho took the lead on the 13th minute before Iwobi leveled the scores for the Super Eagles.
A brace from Victor Osimhen and one from Chukwueze ensured a maximum of three points for the Super Eagles.
Awaziem’s own goal on the 90th minute reduced the deficit for Lesotho, but the win was enough to secure a second win for the super Eagles who beat the Republic of Benin 2-1 at the Godswill Akpabio Stadium in Uyo on Wednesday.
Nigeria will play Sierra Leone next year having six points and top group L.
The three-time African champions are aiming for their 19th appearance in the tournament, after winning their eighth bronze medal in the 2019 edition in Egypt.