The couple found their schedules and an impending cross-country separation too big a hurdle to overcome.
"Zach being away and filming was not easy on them," a source said. "Now he's going to be in New York with his new play. They really loved each other, so it wasn't an easy split."
Quinto, 36, is making his Broadway debut in "The Glass Menagerie" this fall and is best known for his roles as Mr. Spock in the rebooted Star Trek films and in "American Horror Story."
"It just ran its course," the source said. "Zach has been out and about and he seems fine."
He came out publicly in 2011, and he and Groff confirmed their relationship in September.
"He flew to be with her as soon as he heard," another source said. "His heart is broken for her -- and he loved Cory too. The three of them would hang out together."