With their place at the Group C summit already secured, Nigeria boss Eric Chelle made eight changes to his starting XI from the win over Tunisia.
The Super Eagles’ impressive strength in depth ensured that they dominated the first half in spite of that, and only a Samuel Chukwueze miss-kick stopped them from taking the lead inside 10 minutes after some dazzling work down the left wing from Moses Simon.
Victor Osimhen was unsurprisingly a big threat throughout the first half, and he created Nigeria’s first big chance when he surged down the right and pulled back for Paul Onuachu, but he was denied from point-blank range by veteran Uganda stopper Denis Onyango.
There was nothing the 40-year-old custodian could do to stop Onuachu just a minute later, though, as he unsuccessfully attempted to block Fisayo Dele-Bashiru’s cutback, which Onuachu duly turned home for his fourth international goal.
Uganda failed to register a single shot on target before the break, and as none of their previous 14 games had produced over 2.5 goals, their comeback hopes appeared fanciful ahead of the restart.
That was only reinforced when Nigeria continued to dominate, with Chidozie Awaziem and Bruno Onyemaechi going close to doubling their lead.
Having survived those scares, things went from bad to extremely worse for Uganda when Salim Magoola - who replaced the injured Onyango in goal at half-time - rushed off his line and handled outside the area when blocking an Osimhen shot. He was duly sent off, and Nafian Alionzi came off the bench to deputise.
The Cranes’ third goalkeeper of the game didn’t fare any better than the others, and their misery was compounded when Chukwueze found Raphael Onyedika, who surged into the box and slotted through Alionzi’s legs to put the contest beyond all doubt.
The same duo then combined for Nigeria’s third, with Onyedika slotting home in acres of space just inside the box, after Chukwueze had beaten his marker and spotted the midfielder.
A bruising evening at least ended on a positive note for Paul Put’s men when Rogers Mato placed an exquisite chip past Francis Uzoho for a consolation strike.
Nevertheless, just a third defeat in nine meetings meant Uganda finished bottom of Group C, some eight points adrift of Nigeria, who head into the knockout stages full of confidence.
Flashscore Man of the Match: Samuel Chukwueze (Nigeria)