LFC were beaten 1-0 at White Hart Lane but Spurs made organisers aware that they had inadvertently breached regulations and withdrew from the competition.
It means Rodolfo Borrell's Liverpool FC under-19s will now face a mouthwatering semi-final clash with either Barcelona or Ajax, who meet in Spain next week.
A NextGen spokesperson said: “Following conversations with senior Tottenham officials we have agreed to accept their withdrawal from the semi-final stages of the event.
“This is hugely unfortunate and we are sorry to see that such a hard fought encounter as witnessed at White Hart Lane should have this conclusion.
“However, we can only applaud the Club for demonstrating such impeccable levels of sportsmanship and for acting in a manner which recognises the good spirit of both the tournament and the game itself.
“We thank both clubs for their help and support in making this first year of the event such a success and we look forward to re-welcoming Liverpool to the semi-finals.'
It's a welcome slice of good fortune for Borrell's side who outplayed Spurs in midweek but paid the price for a succession of missed chances.
The identity of the player who was ineligible has not been revealed.
Tottenham's director of football administration Darren Eales said: “It is with regret that we have decided to withdraw due to an accidental breach of a competition regulation.
“As a club, we stand for the highest levels of integrity and respect and there was no unfair advantage sought or gained.
“While hugely disappointing for players, staff and supporters, we would like to take this opportunity to thank everyone for their support. We would also like to send Liverpool Football Club our very best wishes for the next round of the competition.”