Liverpool forward Mohamed Salah opened the scoring with a superb free-kick midway through the first half. Aston Villa’s Ahmed Elmohamady then doubled the Pharaohs’ lead before half-time with a powerful drive.
The seven-time winners are also yet to concede a goal at this year’s Afcon, but they rode their luck against Uganda, who was left to rue a string of missed chances.
Uganda’s Farouk Miya and Emmanuel Okwi, who both impressed at the Cairo International Stadium, tested Egypt keeper Mohamed El-Shenawy before Salah broke the deadlock with side’s first shot on target.
And Cranes forward Lumala Abdu was denied twice in quick succession by El-Shenawy before Egypt captain Elmohamady netted his second goal of the tournament with a fine finish from Ayman Ashraf’s cut back on the brink of half-time.
Uganda continued to apply pressure in the second half and Miya twice went close with whipped free-kicks while Okwi’s poked effort clipped the outside of the post with the keeper beaten.
However, Salah did spurn an opportunity to score a third for Egypt when he was denied by a fine one-handed save by Denis Onyango when through on goal.
Egypt talisman Salah was criticized earlier this week for supporting team-mate Amr Warda, whose suspension was reduced by the Egyptian Football Association to the end of the group stage, meaning he is available for the Pharaohs’ next game.
The Cranes finished second in Group A despite their defeat in Cairo, meaning they have reached the Afcon last 16 for the first time since 1978 when they were beaten by Ghana in the final.