Lynch paid tribute to the actor on Friday, posting a photo of his pal on the Twin Peaks: The Return set and writing: "The great Harry Dean Stanton has left us". His last performance will be in a character piece directed by fellow famed character actor John Carroll Lynch that follows a nonagenarian atheist living in a middle America desert town facing up to his mortality.
Outside of his Hollywood life he was a skilled musician, and he spent time playing harmonica and guitar in his own band, the Harry Dean Stanton Band.
Stanton's agent John S Kelly confirmed the star had died on Friday afternoon at the Cedars-Sinai Medical Centre in Los Angeles in a statement. Harry Dean Stanton had a habit of saying goodbye with these words: "Love ya, mean it".
Harry Dean Stanton as "Brett" in Alien.
He began to appear in TV roles before winning a part in his first major film, Cool Hand Luke, in 1967. Acting won, but many years of struggle would pass before Stanton would become a household name.
Two 1984 films cemented his reputation in Hollywood: "Repo Man" and "Paris, Texas". We could see in The Godfather II and Coup de coeur de Francis Ford Coppola, Alien - the eighth passenger of Ridley Scott, The last temptation of Christ of Martin Scorsese, She's so lovely, and Alpha Dog by Nick Cassavetes, ... There is no such person as Harry Dean.
Notably, in 1984 Stanton was given a leading role in Wim Wenders' Paris, Texas.
Stanton was best man at Nicholson's 1962 wedding.
"It doesn't matter", Stanton said, who often greeted interviewers' questions with short answers.
Ebert later conceded that "Dream A Little Dream Of Me", a 1989 film starring Corey Haim and Corey Feldman that featured Stanton as a philosophical neighbor was a clear exception.
He has most recently appeared in this year's revival of Twin Peaks.
Harry Dean Stanton has spent a lifetime in show-business. I loved directing him and I will miss him. His long, craggy face, unkempt hair and off-beat demeanor made him a favorite of directors seeking a character actor to add eccentricity or melancholy to the screen.
Stanton never married, although he has claimed in the past to have "one or two children".