Nigeria still lead the way in Group Three despite their surprise 2-1 loss in Uganda in the 2008 African Cup of Nations qualifiers.Niger recorded their first win in the group on Sunday as they beat Lesotho 2-0 in Niamey.
Both of Niger's goals came in the first half through Hamidou Djibo and Souleymane Sako.
In Saturday's game in Kampala it was two second half penalties that earned Uganda their upset 2-1 win over Nigeria.
Striker Geoffrey Massa won both penalties, the first controversial but the second more legitimate-looking, as Uganda came from a goal down at halftime to revive their hopes of qualifying for the finals in Ghana next January.
David Obua converted the first penalty in the 52nd minute when Egyptian referee Essam Abdelfattah punished Rabiu Afolabi for a legitimate looking challenge on Massa.
Uganda captain Ibrahim Sekagya scored the winner from the spot in the 65th minute after Massa had been brought down by Nigeria goalkeeper Austin Ejide.
The Super Eagles, who lost their 100 percent record and conceded their first goal in the qualifiers, had taken a 25th minute lead through striker John Utaka after he ran onto a perfect pass from captain Nwankwo Kanu.
Striker Yakubu Aiyegbeni had several half chances in the closing stages after Uganda midfielder Noel Kasule was sent off in the 73rd minute for a second caution.
Nigeria's German coach Berti Vogts blamed the loss on poor officiating by the Egyptian referee.
A furious Vogts told BBC Sport: "There was nothing to warrant the first penalty."
"We shall now try to win our next two games against Niger and Lesotho and qualify."
Uganda's coach Laszlo Csaba was all smiles and thanked his team and the 42,000 Ugandan fans for a job well done.
"We gave away a cheap goal in the first half, but responded positively in the second half," he said.
Nigeria play away next in Niamey against neighbours Niger on 17 June when Uganda are away to Lesotho.