In a late addition to the ceremony, Morgan Freeman praised the two-time Oscar winner and his two-time co-star Hackman, five days after the actor and his wife were found dead in their New Mexico.
"This week our community lost a giant, and I lost a dear friend, Gene Hackman," a solemn Freeman said on Sunday night.
"He received two Oscars and more importantly he won the hearts of film lovers all over the world."
Freeman concluded, "Gene always said, 'I don't think about legacy. I just hope people remember me as someone who tried to do good work.' So I think I speak for us all when I say Gene, you will be remembered for that and for so much more. Rest in peace, my friend."
Freeman and Hackman co-starred in 2000's Under Suspicion and in the 1992 Clint Eastwood Western Unforgiven - the movie that earned Hackman his second Oscar.
He won his first for 1971's The French Connection.
The 95-year-old Hackman, his wife Betsy Arakawa and their dog were found dead at their home in Santa Fe on Wednesday.
The cause remains under investigation.
The tone was very different as Oprah Winfrey and Whoopi Goldberg introduced a musical tribute to Jones, who died November 3 at age 91.
"When one hears the name Quincy Jones, one's first thought is musical genius," Winfrey said.
"But the man, our beloved Q, had an equally profound impact on the world of film, as a composer and producer."
Goldberg added, "When we talk about Black excellence, we're talking about Quincy."
They then introduced Queen Latifah, who gave a spirited gospel-style rave-up of Ease on Down the Road, a song from The Wiz, whose soundtrack Jones, a seven-time Oscar nominee, produced.
Jones got a de facto tribute at the beginning of the show when Cynthia Erivo belted out Home from The Wiz in her opening medley with Wicked cast mate Ariana Grande.
Winfrey and Goldberg were cast mates in 1985's The Color Purple.
Jones was a producer of the Steven Spielberg-directed film and co-wrote the score.
Two weeks after his death, Jones was bestowed his second honorary Oscar at November's Governors Awards.
The Hackman segment was followed by the annual "in memoriam" montage of film figures who died since the last Academy Awards.
It included director David Lynch and actors Maggie Smith, Teri Garr, Joan Plowright, Donald Sutherland, Louis Gossett Jr., Shelley Duvall and James Earl Jones.
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