The nearly four-hour service in Los Angeles was marked by speeches, rousing gospel performances and photos of the ever-smiling star of The Green Mile.
Tom and talk show host Jay shared stories about the star and actress Holly Robinson Peete talked about meeting Michael while he was still a celebrity bodyguard.
Stevie appeared via video, solemnly playing piano and singing the opening verses of his life-affirming song As for the man he called "a gentle giant".
Michael died on September 3 at 54, having never fully recovered from a heart attack in July. His doctor was among the speakers at the service at Forest Lawn Memorial Parks and Mortuaries in Los Angeles.
Backed by a gospel choir, singers Angie Stone, Kelly Price, Kenny Lattimore and Abraham McDonald lent their voices to the private funeral.
State Assemblyman Mike Davis and Los Angeles City Council President Herb Wesson also attended, with the council declaring Monday as "Michael Clarke Duncan Day".
Jay said he was touched by the actor's positivity and lack of cynicism. "Just to see such a pure heart and pure kindness, and to see it taken so early," the comedian said, his voice cracking. "There are no sadder words than what might have been."
Other speakers included actors David Boreanaz and Geoff Stults, and Bones creator Hart Hanson.