The hip-hop musical based on the life of Alexander Hamilton, the first Treasury Secretary of the U.S., had been nominated for 16 awards.
Hamilton won the night's biggest award for best musical and actors Daveed Diggs (best featured actor in a musical), Renee Elise Goldberrry (best featured actress in a musical) and Leslie Odom Jr. (best leading actor in a musical) were among the show's actors who won individual honours on the night.
Hamilton creator and lead actor Lin-Manuel Miranda won the award for best original score and delivered an emotionally-charged sonnet dedicated to his wife and victims of the Orlando mass shooting while accepting the award.
The Hamilton company performed the song "Yorktown" at the awards, bereft of the muskets that usually accompany the performance of the song because of the events in Orlando, and closed the evening's awards show with a performance of "The Schuyler Sisters."
The show was hosted by talk-show host James Corden, who began the show with a statement of solidarity with the victims of the mass shooting in Orlando followed by a medley of his favourite musicals.
See the full list of winners here and watch the opening number of the Tony Awards below.