Kimmel said in his Monday night monologue: "The Maga Gang desperately trying to characterise this kid who murdered Charlie Kirk as anything other than one of them and doing everything they can to score political points from it."
The term "Maga" is short for Trump's long-running campaign slogan, Make America Great Again, and many of the US president's supporters often wear caps and shirts bearing the phrase.
The late-night host also noted flags being flown at half mast in honour of Kirk, which got some criticism at the time, and mocked US President Donald Trump's reaction to the shooting.
"This is not how an adult grieves the murder of someone he calls a friend. This is how a four-year-old mourns a goldfish," said Kimmel, who has often poked fun at Trump.
On the day Kirk was shot, Kimmel took to Instagram to condemn the attack and send "love" to the 31-year-old activist's family.
A suspect, 22, has since appeared in court charged with aggravated murder.
Shortly after ABC announced Kimmel had been suspended, President Trump wrote in a social media post: "The ratings challenged Jimmy Kimmel Show is CANCELLED. Congratulations to ABC for finally having the courage to do what had to be done."
Kimmel is one of the top chat show personalities in the US. He has fronted his show Jimmy Kimmel Live! since 2003 and hosted the Oscars four times.