The young Toronto team, which tied Barcelona 2-2 and defeated another Spanish side 5-0 Friday, finished third in its pool after going 1-1-0 Saturday.
The Toronto U12 side lost 1-0 to Ajax before beating Deportivo La Coruna 4-1 with Lowell Wright scoring two goals and Evan Amaral and Charlie Bontis adding singles.
Barcelona then beat Ajax to win Group C with a 3-0-1 record. Toronto and Ajax finished with seven points from 2-1-1 records but the Dutch side finished second by virtue of having beaten Toronto. Only the top two from each of the four groups advance at the 20-team tournament.
The 30-minute games are seven-versus-seven contests played on a smaller field with a smaller goal.
Coach Gianni Cimini's TFC squad qualified for the European event by winning the inaugural U-12 tournament at the Generation Adidas Cup last month in Frisco, Texas.
Toronto defeated FC Dallas in the final of the competition, which featured teams from eight MLS academies, Mexican club Queretaro FC and Club America USA, the U.S.-based affiliate of the Mexican powerhouse.
It's the second year for the under-12 side at the Toronto academy, whose youngest team is under-10.