After its phenomenal success on Broadway, the uplifting musical was awarded the coveted best musical gong, and additional awards for scenic design, lighting, sound and orchestration.
The production's British director, Stephen Daldry, was also given the best director trophy, while the three young stars who take turns to play the title role of Billy – Canadian David Alvarez, and US-born actors Trent Kowalik and Kiril Kulish - jointly won the award for best leading actor in a musical.
Rocket Man singer Elton, who took part in a musical medley during the awards with stars from Broadway shows, missed out on the Tony for top score, but not even that could dampen his mood.
"Thank you for accepting us so beautifully on Broadway," the thrilled star told the audience as he helped accept the best musical award. "We came here at a hard time economically. You opened up your wallets and you opened up your hearts to us. And we love you for it."
Other stars recognised at the annual ceremony, which fetes excellence in American theatre, included Liza Minelli and the late Natasha Richardson, who received a posthumous award.
Guests included Dolly Parton and Anne Hathaway – elegant in a strapless black gown with a voluminous netted skirt. The currently-single Rachel Getting Married actress took her lawyer father Gerard along to the event.