Borle, known to millions for his role on NBC's "Smash," picked up the honor for his performance as the villainous Black Stache in "Peter and the Starcatcher."
"Thank you for making my mom very, very happy with this great honor and for this great moment in time," Borle said.
The play by Rick Elice chronicles the back story behind Peter Pan with Borle playing the part of Captain Hook.
The victory came at the expense of Garfield, who was largely expected to pick up a Tony for his Broadway debut as Biff Loman in the revival of "Death of a Salesman."
Also vying for the statue were Michael Cumpsty ("End of the Rainbow"), Tom Edden ("One Man, Two Guvnors") and Jeremy Shamos ("Clybourne Park").
Borle had been nominated for a Tony previously for his role in the 2007 musical "Legally Blonde."
"Peter and the Starcatcher" earned nine Tony nominations, the most among any play.