The match presented Shawky Garib's men with a final chance to fine-tune preparations for their Africa Cup of Nations qualifying campaign, which gets under way in Senegal on Friday.
Egypt were without a host of key players who ply their trade in foreign leagues, and their under-strength XI found it difficult to break down a Kenya side ranked 66 below them in the FIFA rankings.
The substitute lost his marker before sliding in to meet a Sabri Rahil cross.
Garib will hope for better when a number of his top stars return for next week's Senegal clash.
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