Sayed Hamdi opened the scoring late in the first half and doubled the Pharaohs' lead 18 minutes from time to take his scoring tally in the friendly competition to six goals.
Geddo hit the third for Hassan Shehata's team on 82 minutes while Ceasar Okuhti pulled one back for the visitors shortly afterwards.
Egypt also beat Uganda 1-0 in the group stage.
Kenya won the third-place match 1-0 over Congo earlier in the day.
Stranglehold
Like their previous four matches, Egypt took a stranglehold on the game from the very beginning.
Mohamed Abou-Treika could have netted an early opener when he volleyed a precise Shikabala chip before the linesman signaled for offside.
Ahmed Belal, who bagged a hat-trick in the African champions' 5-1 win over Kenya on January 14th, came close to scoring on 20 minutes.
The Smouha hitman headed an Ahmed Samir Farag cross but his effort went inches above the crossbar.
Four minutes from the half-hour mark, Shikabala tried his luck from distance only to see his fierce shot narrowly go above the top corner of the net.
Hamdi broke the deadlock on 38 minutes after an accurate Farag cross found him unmarked.
The Petrojet man controlled the ball in the box to slot home with no troubles.
A Wael Gomaa blunder could have cost Egypt dearly when the veteran defender failed to intercept a cross, causing one of Uganda's frontmen to strike the post from point-blank range.
Egypt Keep Upper Hand
Egypt expectedly kept the upper hand after the break while their opponents were struggling in vain for fluency.
Hamdi diverted home a low Geddo cross after capitalizing on one of Uganda's recurring defensive lapses.
Geddo, who hit the winner in both teams' previous meeting, could have turned from provider to scorer few minutes later but his powerful shot was competently blocked by the guardian.
He got his name on the scoresheet when he poked into the net from close range, after Ghaly headed a corner kick in his path.
Okuhti scored the consolation goal for Uganda on 84 minutes upon converting a penalty kick.
The spot kick was awarded to the away side because of a Ghaly harsh challenge.