But coach Dave Shannon was happy with his team's performance.
"It is disappointing not to win but I can't be disappointed with our performance as the boys gave it everything," he told the club's official site.
"It has been a fantastic experience for the young lads and the workrate, effort, and standard of football we have shown has been terrific.
"To get the final in a tournament of such good teams is a great achievement and although the Academy is all about development we would have liked to have won it."
Team: Dave Roberts, Callum Woods, Mark King, Jay Spearing (Lee Woodward), Jordan Holmes, John-Paul Kelly, Charlie Barnett, Danny Guthrie, James Frayne, Adam Hamill, Michael Burns (Francis Smith).
How do you think Liverpool's youngsters performed?