Switzerland took the lead after 19 minutes through forward Nevio Scherrer, before Lausanne-Sport midfielder Ethan Bruchez doubled the advantage six minutes before halftime.
Jill Stiel of FC Zürich added a third in the 58th minute to put the match out of reach.
Egypt pulled one back in stoppage time through substitute Anas Roshdy, but it proved only a consolation as the Swiss side secured a comfortable win.
The young Pharaohs reached the knockout stage as one of the eight best third-placed teams across the 12 groups.
They finished third in Group E with four points, three behind leaders Venezuela and two behind England.
Egypt opened their campaign with a 4-1 victory over Haiti, drew 1-1 with Venezuela and lost 3-0 to England.
Switzerland topped Group F with seven points after wins over Mexico and Ivory Coast and a goalless draw with South Korea.
Under the tournament format, the top two teams from each group advance automatically, along with the eight best third-placed teams.
(For more sports news and updates, follow Ahram Online Sports on Twitter at @AO_Sports and on Facebook at AhramOnlineSports.)
Short link: