It also won an emmy for outstanding production design.
The Amazon show looks at how a transgender woman's transition impacts her grown children. The show is nominated in nine Emmy categories this year, including best comedy.
In her acceptance speech, "Transparent" director Jill Soloway called for greater diversity in television.
“It’s a privilege, and creates privilege, when you take people of color, women, trans people, queer people, as the subjects of stories,” she said. “You change the world, we found out.”
“ This TV show allows me to take my dreams about unlikable Jewish people, queer folk, trans folk, and make them heroes. Thank you to the trans community for your lived lives,” she said.
She concluded the speech with a call to "Topple the patriarchy."
Jeffrey Tambor, who plays the lead character, Maura, won the Emmy Award for best comedy actor.
He joined Soloway's call for diversity by asking the industry to give “transgender talent a chance.”
“I would not be unhappy if I were the last cisgender male to play a female transgender on television, we have work to do,” he added.
He thanked Soloway in his acceptance speech: “You changed my life, you changed my career and you changed everything."
This is the second year in a row Tambor has won the best comedy actor Emmy.
Earlier in Sunday's Emmy show Tambor introduced a tribute to the late Garry Shandling whose "Larry Sanders Show" he co-starred in.