The East African side, considered the better in the match, scored in the 80th minute when Faruku Miya’s close range shot from the edge of the box, took a deflection off new boy, Akeem Latifu and sailed into the net.
The late goal turned out to be the party spoiler for Eagles’ Captain, Vincent Enyeama, who was celebrating his 100th cap for the Eagles with the game.
Efforts by the 32 year old Lille goalkeeper to prevent the goal was futile as he was only able to parry the ball into his own net.
Enyeama is the second Nigerian after retired former Everton defender, Joseph Yobo, to make 100 appearances for the Super Eagles.
Both teams agreed to the friendly as part of preparation for the AFCON 2017 qualifiers starting in June.
Although the Super Eagles team was largely made up of new invitees, the loss would have further dampened the spirit of soccer loving Nigerians as the loss puts Uganda ahead of Nigeria in a head-to-head.
The Ugandans were ranked 71 in the world.
The Eagles leave for Nelspruit, South Africa on Thursday where they will face the Bafana Bafana in another friendly match on Sunday.