Stewart, 52 hosted the Comedy Central show since 1999. In his last episode, he made an impassioned final speech warning his audience against falsehood that is "designed to obscure and distract".
"So, whenever, something's been titled Freedom Family Fairness Health America take a good long sniff. Chances are it's been manufactured in a facility that may contain traces of bull***t," he said.
But before the final goodbye, came a moment that celebrated the many achievements of the man, who, as Stephen Colbert put beautifully, was "infuriatingly good at his job".
"You said to me and many other people here years ago 'never thank you because we owe you nothing'. That's the few times I have known you to be dead wrong. We owe you not just what you did to our careers by employing us on this tremendous show that you made. We owe you because we learnt from you," Colbert said, bringing Stewart to tears.
"We learnt from you... How to work with clarity, how to treat people with respect. You were infuriatingly good at your job. All of us who were lucky enough to work with you for 16 years are better at our job because we got to watch you. We are better people for having known you. You are a great artiste and a great man."
President Barack Obama, who appeared on the show recently, had called Stewart a "great gift to the country".
"You've been a great gift to the country," -President Obama to Jon Stewart on @TheDailyShow #JonVoyage
Hillary Clinton echoed similar sentiments in her tweet, saying, "Missing Jon Stewart already. #GOPdebate #JonVoyage -H."
The show also included testimonials from Craig Kilborn (Stewart's predecessor), John McCain and Bill O'Reilly.
Rocker Bruce Springsteen gave Stewart a perfect send-off by taking to the stage to perform on "Land of Hope and Dreams" and "Born to Run" with E Street Band.
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