 Kanu's goal separated the Group Three rivals in a tense affair |
Nigeria beat Group Three rivals Uganda 1-0 in Abeokuta on Saturday to hand coach Berti Vogts a win in his first competitive match.
Nigeria have now won all three of their Nations Cup qualifiers, and their nine points are five more than second-placed Uganda.
On Sunday, Lesotho lifted themselves off the bottom of the table when beating Niger 3-1 in a stormy match in Maseru.
The hosts' first win of the qualifying campaign was enough to leapfrog their rivals into third spot.
Lesotho took the lead after 16 minutes as Refiloe Potse scored in a goalmouth scramble but Daouda Kamilou replied for the visitors on the half-hour with Niger's first Group Three goal.
A minute before the break, Potse grabbed his second with a glancing header to send Lesotho into half-time 2-1 up to the delight of the 5,000 watching fans.
The game was in the balance until the 70th minute when Niger's Djiri Boukary was sent off.
The dismissal precipitated a long stoppage during which the visitors verbally abused match officials and threatened to leave the pitch.
 | We played against a very good and organised Ugandan team Nigeria coach Berti Vogts |
Lesotho took full advantage eight minutes later as full back Mpitsa Marai wrapped up the points.
On Saturday, Nigerian forward Nwankwo Kanu scored the all-important goal against the Cranes after 73 minutes in a tight affair between the group leaders and the team in second place.
But the Super Eagles' German boss Berti Vogts can count himself fortunate to have the points after Uganda's Cranes had a goal disallowed in the last minute.
"I was not happy with the first half. We did not play very well," said the German coach, who before the game had called on Nigeria to win in style against the visiting Ugandans.
"We had a better second half but overall, it was not very good."
Uganda suffered their first defeat in Group Three after a late goal was disallowed by Senegalese referee Diatta Badara for an infringement.
Cranes players surrounded the referee after the final whistle, bitterly complaining that the goal should have stood.
"This was a draw," said Uganda coach Lazslo Csaba.
"Against Niger in another Nations Cup tie, we had a Senegalese referee and we played against that referee. It was the same thing against Nigeria.
"There were two very good teams playing football but the referee was not good."
Kanu's goal came after he found the back of the net during a goalmouth melee in the Uganda box following a corner from Chelsea's John Obi Mikel.