Despite dominating the game, Semi Ajayi's late equalizer spared Nigeria's blushes after a Motlomelo Mkhwanazi opener.
The result increases the pressure on Super Eagles coach Jose Peseiro, especially with the Africa Cup of Nations just months away.
The absence of injured striker Victor Osimhen was notably felt as Nigeria lacked a cutting edge against Lesotho.
Meanwhile, Egyptian football star Mohamed Salah showcased his goal-scoring prowess by netting four times as Egypt secured a commanding 6-0 victory over Djibouti in the opening match of the African 2026 World Cup qualifiers.
Salah's stellar performance took his international goal tally to an impressive 53 goals in 93 games.
The Liverpool forward played a pivotal role in Egypt's quest for a spot in the expanded 2026 World Cup.
In other matches, Mozambique secured a rare away win against Botswana in Group G, while Algeria struggled to a 3-1 victory over Somalia, prompting coach Djamel Belmadi to make halftime substitutions, including stars Riyad Mahrez and Amine Gouiri.
Burundi marked their first game with a 3-2 win against the Gambia in Tanzania, and Sudan and Togo played to a 1-1 draw in their Libya-hosted clash.
Cape Verde and Angola failed to capitalize on their Group D opener, settling for a goalless draw in a match filled with missed chances.
With 40 African teams vying for nine direct World Cup spots and one inter-confederation playoff place, the competition's stakes are high from the outset.
The opening rounds continue this week before resuming in June 2024.