As Kimmel walked on stage he quipped: "Oh good, I got a sitting ovation," and Timberlake was seen jokingly skulking out of the way.
Kimmel later told Timberlake that if his former bandmates in 'N Sync were watching, they'd let him back into the band.
Timberlake's performance earned a mixed reaction on Twitter.
Earlier, Timberlake said the beginning of the Oscars would be free of politics.
He said: "Watch the top of the show, it will be very un-political. I can promise you that."
It was an apparent tease to Timberlake's performance of his Oscar-nominated song, Can't Stop the Feeling, which is from the animated film Trolls.
Timberlake said he was happy the academy honoured such a feel-good song. "I think the world could use a little bit of that."
Politics is on the mind of many nominees at today's ceremony. Some top nominees, including Ruth Negga and director Barry Jenkins, were seen wearing blue ribbons supporting the American Civil Liberties Union.
Others, including documentary nominee Ava DuVernay and best actor nominee Andrew Garfield, say art is inherently political and winners should express their feelings about the current political climate if they wish.
- With AP
