كتب : وكالات
Hani Ramzi's side had won the first leg 2-0 and thus a loss by a one-goal margin was enough for them to go through.
Batswana took a two-goal lead before Marawan Mohsen pulled one back upon heading home a lengthy throw-in, to give Egypt a 3-2 aggregate win.
The young Pharaohs carved out a number of clear-cut opportunities in the first half but failed to translate their dominance into goals.
Shehab Ahmed could have ended the game in a draw after one of his trademark thunderbolts went just past the right post.
"Today's game was a tough lesson for the (Egyptian) players. They should learn not to waste so many clear-cut scoring chances," head coach Ramzi said after the match.