Perry, 26, went down 3-0 (11-6 11-3 12-10) to the 21-year-old from Egypt.
Sherbini, the defending champion, was on top for the first two games but was made to battle to take the third against Perry, the world number eight.
Perry was beaten by compatriot Laura Massaro in the final of the British Open last month.
World number two Massaro faces Egypt's third seed Raneem El Welily in the quarter-finals on Wednesday.
Britain's Sarah-Jane Perry lost to world number one Nour El Sherbini in the quarter-finals of the women's World Championship in Egypt.