In Las Vegas, Cruise bowed his head in the cavernous theatre, which was packed with movie theatre owners and others who work in the industry.
"Thank you, Val - wish you well on your next journey," Cruise said afterwards.
Cruise was speaking during the Paramount Pictures presentation at CinemaCon. He also showed off a sneak peek trailer of Mission: Impossible - The Final Reckoning, which is set to be released later this year, and honoured the film's director Christopher McQuarrie, who was named CinemaCon's director of the year.
The trailer showed Cruise, who is famous for doing his own stunts, in a series of action-packed scenes - on fighter jets, in explosions and wing walking on a vintage plane.
As Hollywood paid tribute to Kilmer, Cruise had been one of the few stars who waited to publicly comment on the actor's death.
The star has been vocal about how much he enjoyed working with Kilmer. He said on Jimmy Kimmel Live! that he cried having him on set for Top Gun: Maverick.
"I was crying, I was crying. I got emotional," Cruise said on the show about working with Kilmer. "He's such a brilliant actor. I love his work."
Kilmer's family told US media that he died after coming down with a pneumonia. The actor had two tracheotomies while undergoing treatment for throat cancer.
The procedures forced him to use a voice box to speak, and in the 2022 film, he types on a screen to communicate with Cruise's character. Toward the end of their scene together, Kilmer's Iceman gets up from his chair and coarsely tells Cruise: "The Navy needs Maverick".
The two embrace and then Iceman pokes fun, questioning Cruise about who is the better pilot.