The long-awaited drama (it was shot three years ago) of creation and one family's place in it drew a scattering of harsh, prolonged boos, answered by enthusiastic applause from others.
It is Malick's fifth film in a nearly 40-year career, and his first at Cannes since 1979's "Days of Heaven," which earned him the festival's directing prize.
Malick, who is notoriously press-shy, skipped out on the press conference that followed Monday's screening, leaving Pitt, Chastain and his producers to face reporters.
"Mr. Malick is very shy, and I would say that I believe his work speaks for itself," producer Sarah Green said.
Pitt, who is expected to attend the film's official festival premiere Monday night with partner Angelina Jolie, compared Malick's attitude toward publicizing a film to building a house - the builder is not then expected to sell it.
"I don't know why it's accepted that people who make things in our business are then expected to sell them, and I don't think that computes with him," Pitt said. "He wants to focus on the making of it, not the real estate, selling the real estate. It is an odd thing for an artist to start something and then be salesman."
Cannes organizers had hoped to debut the film a year ago, but it was not ready in time.
"The Tree of Life" stars Pitt as a loving but sometimes brutally stern father, with Chastain the wife who stands as a figure of grace for their three confused, intimidated sons. Penn plays the eldest son as a grown man, reflecting on the people and moments that shaped him.
The richly personal drama is told in a vast reach of impressionistic exchanges and images: from breathtaking views of the universe's creation to primordial scenes in the age of the dinosaurs to tender and terrifying family moments.
Some at Cannes found it all deeply moving. Others said Malick went over the top as some cosmic sequences play on for 15 minutes or more without a human face to be seen.
The range of reactions might suit Malick just fine.
"One of the reasons Terry maybe shies away from forums like this is that he wants the work to stand on its own. He doesn't want to say what it's about or whether it's autobiographical or not," said producer Bill Pohlad. "He just wants the audience to bring their own thing to it ... as opposed to him interpreting it or verbalizing it."