The openly gay 35-year-old, who plays Danny Baker in the NBC sitcom, denounced the offensive comments made by Morgan at a stand-up gig in Tennessee on Friday.
The comedian later apologised for the misjudged material, insisting: "I'm not a hateful person and don't condone any kind of violence against others."
In the wake of the scandal, Jackson released a statement to Out saying: "I am disgusted and appalled by Tracy Morgan's homophobic rant. The devastating repercussions of hate-filled language manifest in very real ways for today's LGBTQ youth.
"I've known Tracy for two years, spent many long hours with him on set, and I want to believe that this behaviour is not at the core of who he is. I'm incredibly disappointed by his actions, and hope that his apology is sincere."
30 Rock creator Tina Fey previously described Morgan's anti-gay comments as "disturbing", while NBC chairman Bob Greenblatt warned that his behaviour "will not be tolerated".
Morgan initially received the backing of comedian Chris Rock, but the Grown Ups star has since accepted that the 42-year-old said "s**t [that] wasn't called for".