He even went as far to wear a disguise when he left Washington for Los Angeles, where the Emmys are held, possibly including fake facial hair.
"This was an attempt to poke a little fun at myself and add a little bit of levity to the event," Spicer told the Times.
Once in Los Angeles, he reportedly stayed in his hotel room, only taking part in one closed door rehearsal in front of as few people as possible. His name also didn't appear on Emmys scripts.
Colbert reportedly suggested the joke himself, and managed to get Spicer to agree through his producer at CBS, who knew Spicer.
His joke has been widely criticised. For many, it was an attempt to "normalise" a former White House Press Secretary who "repeatedly" and "blatantly" lied to the American people on behalf of President Trump.
Spicer's jokes stirred many angry reactions on Twitter within moments of him leaving the stage, according to Washington Post.
"NO to Sean Spicer," journalist Mark Harris tweeted. "It's so great that we can embrace someone who used a powerful position to abuse the press and lie to America."
"Do NOT cheer for Sean Spicer," tweeted Kelly Dittmar, an assistant professor at Rutgers University. "This is how we normalize & excuse unethical, racist, sexist, etc. behavior."
Others, including author and commentator Roxane Gay, argued that Spicer's appearance reflected white privilege.
Others saw Spicer's act as an attempt to knock Trump.
"Colbert couldn't leave the stage without finding some special way to hit the president where it really hurts," Vanity Fair's Laura Bradley wrote on Sunday. "So he brought out his secret weapon: Sean Spicer."
In his New York Times interview, Spicer commented on the social media backlash, saying that people are reading too much into things.
- NZ Herald with Washington Post, AP