The show, which was nominated for 10 Tony Awards, opened at the ART in August and is currently running on Broadway.
Producer Jeffrey Richards mentioned Harvard in his acceptance speech and said that Diane Paulus, the show's director and a theater professor at Harvard, "gave us a great home to incubate this show at the American Repertory Theater."
Audra McDonald took home the award for Best Performance by an Actress in a Leading Role of a Musical—her fifth Tony—for her portrayal of Bess.
In an emotional acceptance speech, McDonald described the impact that theater had on her when she was nine years old.
"I was a little girl with a pot belly and Afro puffs, hyperactive and overdramatic, and I found the theater and I found my home, and I found a place to express myself...and to think that the theater was so good to me is mind-blowing," she said.
The musical "Once," which won eight Tony Awards, including Best Musical, also spent its workshop period at the ART.