Mohammed Salah’s superbly taken free kick in the 10th minute sent the Pharaoh’s top of Group D on seven points with Ghana finishing as runner up with six.
Egypt were awarded a free-kick after a clumsy challenge by John Boye on Abdallah El Said and Salah stepped up to hammer the ball through the wall and leave Ghana goalkeeper Razak Brimah with no chance.
It was the third successive clean sheet for Egypt who are playing in the tournament in Gabon after a seven-year absence.
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“Our goal was always to win the match, we never go into a match with the intention to draw,” Egypt coach Hector Cuper told reporters.
“I would have liked a better second half but we were playing a very strong opponent.”
The seven-times African champions will now play North African counterpart Morocco in the quarter-finals in Port Gentil on Sunday while Ghana travel to Oyem to face the Democratic Republic of Congo on the same day.
In the other game of the day, Uganda broke their 39-year Afcon finals goal drought as Farouk Miya scored to hold Mali to a 1-1 draw in Oyem.
Miya opened the scoring with a rising shot into the top corner, while Mali, five-times semi-finalists, levelled proceedings when 20-year-old Yves Bissouma’s 30-yard free-kick flew into the net.
Uganda last played at the tournament in 1978.