Stanton passed away Friday at Cedars-Sinai Medical Center in Los Angeles.
Stanton, whose gaunt, worn looks were more recognizable to many than his name, appeared in more than 100 films and 50 television shows, including the films "Alien" and "Repo Man" and the series "Big Love" and the recent version of "Twin Peaks."
For many years, Stanton played lesser-billed characters. In 1984, he got his first part as a leading man in "Paris, Texas," which won a host of awards, including the Palme d'Or at the Cannes Film Festival.
The late film critic Roger Ebert wrote of the actor in 1989, "No movie featuring either Harry Dean Stanton or M. Emmet Walsh in a supporting role can be altogether bad."
Stanton often played haggard men with battered souls, Turner Classic Movies said in its description of him. TCM is owned by CNN's parent company, Time Warner.
"A restless, unconventional spirit off-camera, Stanton always lent a sympathetic realness to the menacing criminals and barroom-dwelling outsiders he stashed beneath his craggy face and wiry, worn frame," TCM said.
Well-lined face was 'the story'
Writer and director David Lynch said in a statement that Stanton was a great human being as well as a great actor.
"There went a great one. There's nobody like Harry Dean. Everyone loved him," he said.
Lynch appeared in the 2012 documentary "Harry Dean Stanton: Partly Fiction."
"How would you like to be remembered?" Lynch asked.
"It doesn't matter," Stanton said, who often greeted interviewers' questions with short answers.
In the film, playwright and actor Sam Shepard (who died in July) said that Stanton realized his well-lined face was "the story."
"You read all kinds of things into it," Shepard said.
Stanton once said he didn't blame anyone for the kinds of parts he was given early in his career.
"I hated being typecast in those roles. It was personally limiting, only playing stereotyped heavies," he said to The Sydney Morning Herald in 1987. "But I got those roles because I was angry, because that's what I projected ... and I had an extreme lack of self-confidence."
He told the Australian newspaper he had changed by adhering to Eastern mysticism, which helped him become more self-aware and less angry.
Ed Begley Jr., who worked with Stanton on several projects, had been friends with him since the 1970s.
"Just lost my friend of the past 45 years. Harry Dean Stanton. My heart is broken, but at 91...a life well lived," Begley tweeted.
James Woods wrote: "Saw this and I just jumped up out of my chair. I am devastated. I loved Harry Dean. Loved him. So much. OMG. #RIPHarryDeanStanton."
Born in Kentucky
Stanton was born in Kentucky in July 1926. His father was a tobacco farmer and had an often-strained relationship with the actor's mother. Stanton served in the Navy during World War II, then went to the University of Kentucky.
He was indecisive on a course of study until he found the drama department but still he didn't graduate. He told The New York Times it was by choice.
"I thought that was a positive, independent kind of statement," he said in 1986. "I never liked being ordered around, which, of course, was an overreaction. I eventually found out that I didn't mind being ordered around at all when it was by someone who knew what he was doing.''Stanton eventually moved to New York to become an actor in a traveling children's theater show.
By the mid-1950s he was in Hollywood where he was cast for the first time as a background player. He appeared in many memorable films -- "The Godfather: Part II," Pretty in Pink," "The Last Temptation of Christ," "The Green Mile" among them.
Stanton never married but is survived by family.