Toni Fernandez, who signed with Barca earlier this month after turning 16, flicked in a left-footed shot past reserve City goalkeeper Stefan Ortega to give the German managers side a 4-1 win on penalties.
Barcelona kicked off their US tour in the pre-season contest against the four-time reigning Premier League champions, guided by former Barcelona player and coach Pep Guardiola.
A sellout crowd of 63,237 spectators were unhappy early as a storm delayed the start by 80 minutes, but were delighted with a strong early pace, before both teams gave reserve players abundant time on the pitch.
Barcelona jumped ahead 3-0 on penalty kicks thanks to a left-footed shot by Alejandro Balde before Amar Ahmed kept City in it by beating reserve Barca goalkeeper Ander Astralaga, setting the stage for the teen newcomers heroics.
Pau Victor had opened the scoring in open play for Barcelona in the 24th minute, taking a quick through ball pass from Marc Casado and firing a right-footed blast from the right side into the goal.
