Geddo, who replaced Mohamed Abou-Treika, gathered the ball in the area to score the winner with an unstoppable effort.
Egypt's veteran defender Wael Gomaa celebrated his 100th cap in the game when he was introduced on 63 minutes.
Hosni Abd-Rabou was included in the Pharaohs' starting eleven for the first since recuperating from his cruciate ligament injury.
Hosts Egypt are now on top of the friendly competition's Group A with six points, three ahead of second-placed Uganda.
Tanzania and Burundi, who played out a 1-1 draw earlier on the day, lie third and fourth respectively with a single point each.
Egypt won all their six matches against Uganda.
Offside Trap
Uganda successfully depended on the offside trap most of the game to keep a clean sheet amid Egypt's onslaught.
Ahmed Belal could have opened the scoring on 28 minutes from a one-on-one opportunity but was caught offside.
The second scoring chance fell to defender Mahmoud Fathallah when he connected with an Abou-Treika cross only to see his header go past the post.
The visitors' strategy once again paid off when Ismaili's Ahmed Samir Farag hit a goal that was disallowed for offside.
Al-Sayed Hamdi beat the offside four minutes from the hour mark to go clear but his poor shot went wide of the mark.
The introduction of Geddo notably injected zeal.
He first came close to scoring on 70 minutes when his fierce header narrowly missed the target.
But eventually the Ahli forward managed to snatch a late goal that was enough for the African champions to emerge winners.
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Video: Last-gasp Geddo gives Egypt win over Uganda