"Kinky Boots" star Billy Porter earned the prize for Best Actor in a Musical, while the show also earned the accolades for Best Sound Design, Orchestrations, Score and Choreography at Radio City Music Hall Sunday night.
The show, which featured music by pop star Cyndi Lauper, went into the competition nominated for a leading 13 awards.
"Matilda," a stage adaptation of Roald Dahl's children's book about a young girl trying to save herself and her classmates from an evil school headmistress, was up for 12 prizes. It won for Best Book, Scenic Design of a Musical, Lighting Design in a Musical and Featured Actor in a Musical for Gabriel Ebert.
Christopher Durang's "Vanya and Sonia and Masha and Spike," a comedy about a dysfunctional family in rural Bucks County, Pa., won the Tony for Best Play.
Edward Albee's scathing relationship drama "Who's Afraid of Virginia Woolf?" was declared the Best Revival of a Play. Pam MacKinnon picked up the award for Best Direction of a Play and Tracy Letts the prize for Best Actor in a Play.
"Pippin" earned the title for Best Revival of a Musical. The medieval circus-themed show's ringmaster Patina Miller won for Best Actress in a Musical and her co-star Andrea Martin scored the Tony for Featured Actress in a Musical. Diane Paulus picked up the trophy for Best Direction of a Musical for directing "Pippin."
Cicely Tyson garnered the Best Actress in a Play award for "The Trip to Bountiful," Courtney B. Vance won the statuette for Featured Actor in a Play for "Lucky Guy" and Judith Light went home with the Featured Actress in a Play prize for "The Assembled Parties."
The CBS telecast of the prize presentation featured performances by the stars of "Kinky Boots," "Matilda," "Newsies," "Once," "Bring It On," "Annie," "Pippin," "Spider-Man: Turn Off the Dark," "Motown," "The Phantom of the Opera" and "A Christmas Story." Neil Patrick Harris served as host of the awards show.
New York City Mayor Mike Bloomberg said during the ceremony 11.6 million people attended shows during the 2012-13 Broadway season.