The youngster's achievement matches him with past back-to-back winners Wayne Rooney, Robbie Fowler and Ryan Giggs.
The 21-year-old beat team-mate Harry Kane, along with Everton striker Romelu Lukaku, Burnley defender Michael Keane, Sunderland goalkeeper Jordan Pickford and Manchester City winger Leroy Sane.
Alli could consider himself unlucky not to be shortlisted for the senior award too, having contributed 16 goals from midfield as Tottenham again battle for the Premier League title.
Mauricio Pochettino said earlier this month: "I think he deserves [to be nominated] because he's showing great performances every week and in every game.
"He's improved a lot from last season. I think he's a better player, he's showing better stats and in my opinion yes, he deserves it.
"After his first season in the Premier League always the people want to see again in the second season if he can confirm all that he showed last season.
"Not only did he confirm that, he's improved in all aspects of his game. That means he's clever, intelligent, still with the potential to improve and learn and today he's showing that he's one of the best players in the Premier League."
Alli's success continues an incredible run for Spurs in this category.
The north London outfit have now won the men's young player award in five of the last six seasons - Kyle Walker in 2012, Gareth Bale in 2013, Kane in 2015 and Alli in 2016.
Only Chelsea's Eden Hazard in 2014 has interrupted Spurs' winning streak