The Leopards will now wait to see if they can grab one of the four places for the third placed teams.
Uganda started the game quite well and looked like the fancied side to get on the scoresheet.
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.
"We don't care who we are playing in the next round, whether it's Kenya or Senegal".
Egypt were dealt an early blow as Ahmed Hassan who had earlier suffered a kick on the calf by Khalid Aucho, was stretchered off on 25 minutes and replaced by Morwan Moshen.
Burundi, though, nearly took the lead seven minutes later when Pierre Kwizera fired in a superb 30-yard effort that was tipped over by Ibrahim Kone. Salah then turned the tide toward the record seven-time African champions by lifting a free-kick over a defensive wall and past goalkeeper Denis Onyango into the corner of the net. Farouk Miya could have scored for Uganda after 55 minutes but his shot missed the target.
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Uganda's first change came through injury in the last 20 minutes, as Onyango went off for Robert Odonkgara.
DR Congo thumped Zimbabwe 4-0 in Cairo, with Zimbabwe's problems beginning just before kick-off when goalkeeper George Chigova was injured during the warm-up and Elvis Chipezeze stepping in for the Group A match.
"We have a good coach". This gives us morale boost to continue our way in the tournament. Two years ago under Milutin Sredojevic, they were close to securing a point but Abdallah El-Said scored in the dying seconds to give Egypt the win. The first goal opened the match and then we settled things before halftime. Elmohamady said: 'Nine points out of three games is something Egypt is used to - the hard part is what comes next. They combined physicality with positivity, putting together some nice passing moves.
"The result is not good, but I am very proud of my players".
I feel disappointed for the result.
Physicality isn't the dirty, nasty play you sometimes see of trying to stop people - it's physicality that sets up attacks.