Farouk Miya gave the East Africans a surprise victory at the Akwa Ibom International Stadium in Uyo after Enyeama parried but couldn’t keep out his 81st-minute shot.
Uganda was only a late replacement for Bolivia, which pulled out of the game over fears of an attack by Nigeria’s Boko Haram extremist group.
The friendly was meant to start Nigeria’s preparations for 2017 African Cup of Nations (AFCON) qualifying after the 2013 African champion surprisingly missed out on this year’s continental championship.
But there were more problems than solutions for assistant coach Daniel Amokachi, who was in charge of the team while head coach Stephen Keshi continues to negotiate a new contract with the federation.
Nigeria’s attack was toothless until teenager Moses Simon, one of three players making debuts, was introduced in the second half. He had two good chances but couldn’t make the breakthrough and Miya pounced at the other end, with his shot looping into the net after being half-blocked by Enyeama.
“A great disappointment, but this is football,” Enyeama said.
The 32-year-old was presented a trophy to mark his centenary at half time by Akwa Ibom Governor Godswill Akpabio and NFF president, Amaju Pinnick.
Nigeria next travel to Nelspruit to face South Africa on March 29 in another friendly encounter.
Both countries last met in November 2014 at the Uyo Stadium where a 2-2 draw meant South Africa prevented Nigeria from qualifying for AFCON 2015 in the presence of an utterly dejected Akpabio.