The 34-year-old singer previously dedicated a song to the late actor while performing in Los Angeles on the night he was found dead in his California home earlier this month. At the time, Bareilles performed her track "Hercules" for the comedian.
Emmy producer Don Mischer said in a statement the event organizers felt they "need to do something powerful and memorable" to commemorate Williams. He said Crystal "seemed like the perfect choice" for the task given his longtime friendship with the Mrs. Doubtfire star.
The 2014 Emmy Awards will air August 25 on NBC.