"It was never my intention to make light of the murder of a young man. I don't think there's anything funny about it," Kimmel told his audience, his voice choking with emotion.
"Nor was it my intention to blame any specific group for the actions of what was obviously a deeply disturbed individual - that was really the opposite of the point I was trying to make," he added.
Disney, parent company of the ABC network which airs Jimmy Kimmel Live!, halted production of his show on September 17, two days after Kimmel said in his opening monologue that President Donald Trump's supporters were desperate to characterise Kirk's accused assassin "as anything other than one of them" and accused them of trying to "score political points" from his killing.
Before Kimmel's show aired on Tuesday, Trump wrote that he "can't believe" ABC gave Kimmel back his show, and hinted at further action against the network.
"Why would they want someone back who does so poorly, who's not funny, and who puts the Network in jeopardy by playing 99% positive Democrat GARBAGE," Trump wrote Tuesday on Truth Social.
"He is yet another arm of the DNC (Democratic National Committee) and, to the best of my knowledge, that would be a major illegal Campaign Contribution. I think we're going to test ABC out on this."
The Trump administration and many of its supporters were enraged by Kimmel's comments of last week, which occurred five days after Kirk, a close Trump ally and radio-podcast host, was shot dead while speaking on the campus of Utah Valley University in Orem, Utah.
In response to Kimmel's remarks, the Federal Communications Commission chairman, Brendan Carr, threatened an investigation and urged television stations to drop Kimmel's show or face possible fines and revocation of their broadcast licenses.
Disney's decision to cut short Kimmel's exile marked a high-profile act of defiance in the face of an escalating crackdown by Trump on his perceived media critics through litigation and regulatory threats from the FCC.
Even though Disney has now brought back Kimmel to ABC's lineup, the two largest television station groups of ABC local affiliates - Nexstar Media Group and Sinclair - are still boycotting his show.
Kimmel, a four-time Oscars host, said Trump was not just after comedians he disliked, but also journalists, saying of the Republican president: "He's suing them, he's bullying them".
"I know that's not as interesting as muzzling a comedian, but it's so important to have a free press, and it is nuts we're not paying more attention to it," Kimmel said.
He also said he was "deeply" moved by the forgiveness expressed by Kirk's widow, Erika Kirk, for her husband's accused killer, a 22-year-old technical school student from Utah.
with PA
