"Our hearts are with the staff of Charlie Hebdo and their families tonight," the host of "The Daily Show" said, after a long silence and nervous laughter.
"I know very few people go into comedy as an act of courage, mainly because it shouldn't have to be that," Stewart continued. "But those guys are Hebdo had it, and they were killed for their cartoons," he said.
Stewart said the killing of at least 12 people at the paper's offices was a reminder that the institutions and politicians he ridicules each night "are not in any way the enemy."
"It's still a back and forth between those on, let's call it, 'Team Civilization,'" he said.
Watch the clip, courtesy of Comedy Central: