It happened Monday during the invocation.
The unidentified man said just a few words about loving Yale before he was grabbed by security and taken away.
It was not clear if the disruption had anything to do with a union demonstration outside the commencement.
A large group of graduate teachers and their supporters marched to demand that the Ivy League school begin negotiations with their newly formed union.
The union supporters said they had no plans to disrupt the graduation and were there to bring attention to the labor dispute.