Neil Patrick Harris hosted the event for the fourth time. The show opened with a big, splashy opening number which included ex-boxer Mike Tyson dancing and glitter guns.
The feel-good musical "Kinky Boots" featuring Cyndi Lauper and Broadway veteran Harvey Fierstein took home the most awards including best musical, best performance by an actor in a leading role in a musical, best orchestrations, and best original score.
"Kinky Boots" beat "Matilda the Musical" for the most coveted award - top musical. The musical led the bunch with 15 nominations. The show is based on an obscure 2005 British film about a British shoe factory on the brink of ruin that retrofits itself into a maker of footwear for drag queens.
Christopher Durang's comical "Vanya and Sonia and Masha and Spike" won the best play Tony.
"Matilda the Musical" won four awards including best performance by an actor in a featured role in a musical.
Three other shows - "Pippin," ''Who's Afraid of Virginia Woolf?" and "The Nance" - shared three awards each.
The biggest star with a nomination was Broadway newcomer Tom Hanks, but he lost to Tracy Letts of "Who's Afraid of Virginia Woolf?"
The nominators ignored some big-name talent who graced Broadway stages this season, including Bette Midler, Jessica Chastain, Al Pacino, Katie Holmes, Paul Rudd, Alec Baldwin, Alicia Silverstone, Sigourney Weaver, Cuba Gooding Jr. and Scarlett Johansson.
Presenters included some of the A-listers overlooked for nominations as well as Jesse Eisenberg, Jon Cryer, Jake Gyllenhaal, Anna Kendrick, Zachary Quinto, Sally Field, Audra McDonald, Alan Cumming and Jesse Tyler Ferguson.
The Tony winners were picked by 868 Tony voters, including members of The Broadway League, American Theatre Wing, Actors' Equity, the Dramatists Guild, Stage Directors and Choreographers Society as well as critics from the New York Drama Critics Circle.
The Associated Press contributed to this report.