The comedian made reference to Brown's arrest for domestic violence against former girlfriend Rihanna in 2009, after host Matt Lauer used an unfortunate choice of words.
When the show returned from a commercial break, Lauer said: "We're hoping the same kind of weather hits us tomorrow when we've got Chris Brown out on the plaza."
Shocked, Rock joked: "Did you say you hope the same weather hits you?
"I hope some weather doesn't smack us upside the head."
The presenters responded with awkward laughter while Sesame Street's Elmo - who was appearing as a guest to talk about the Olympics - broke the tension by saying: "Elmo will try to make it wholesome."
Rihanna has recently stated that she wasn't expecting such a negative reaction to her decision to collaborate with Brown on a new track.
Watch Chris Rock and Elmo on The Today Show below: