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.
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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:
