Crystal took the stage just after singer Sara Bareilles sang "Smile" during the in memoriam portion of the show. Williams' suicide earlier this month had shocked his friends as well as his legion of fans.
"He made us laugh hard, every time you saw him," Crystal said, speaking in front of a large image of Williams. "His brilliance was astounding... I used to think if I could just put a saddle on him and stay on for eight seconds I would be OK."
"As genius as he was on stage, he was the greatest friend you could imagine," Crystal said. "It's very hard to talk about him in the past, he was so present in all our lives … for 40 years, he was the brightest star in the comedy galaxy."
Crystal closed by saying that even though Williams is gone, his "beautiful light will continue to shine on us forever, the glow will be so bright it will warm your heart."
A short video of some of Williams' hilarious appearances on stage and screen played right after, then the stage went quiet and the Emmys faded to black before a commercial break.
"We felt we needed to do something powerful and memorable. Billy seemed like the perfect choice," he told E! News last week.
Crystal and Williams were friends for decades before Williams died Aug. 11 at the age of 63.
The organization's slogan read, "Where there's laughter, there's hope."
When Crystal learned of the news of his dear friend's death, he took to Twitter and posted, "No words," which was seconded by Goldberg, who wrote "BillyCrystal is right...There are No words."
But Crystal found the right words tonight to honor someone with whom he worked for decades.