Security concerns there caused officials to suggest they work elsewhere. So with the exception of a few background scenes shot in Pakistan, "A Mighty Heart" will be made in the western Indian city of Pune.
The Oscar-winning U.S. actress plays the slain reporter's wife, Mariane. Pitt, Jolie's partner, is the movie's producer.
"I am disappointed that we could not shoot the film in Pakistan, a country that I love and have visited three times," said Jolie in a statement issued on Saturday by Trevor Neilson, an adviser to the couple.
"They talked with people from all levels of the Pakistan government and there's certainly no hard feelings. But it became clear that it was preferable to film in India," Neilson told Reuters by telephone.
He said there was no release date set for "A Mighty Heart," which is being made by Pitt's production company, Los Angeles-based Plan B.
The film is based on a book by Mariane Pearl, "A Mighty Heart: The Brave Life and Death of My Husband Danny Pearl."
Pearl, a 38-year-old reporter with The Wall Street Journal, was kidnapped in Karachi in early 2002 while researching a story in the aftermath of Sept. 11. A videotape of Pearl having his throat cut was later circulated by his killers.
English filmmaker Michael Winterbottom, famed for such war-based films as "Welcome to Sarajevo" and "The Road to Guantanamo," is directing the movie.
In her statement, Jolie said "A Mighty Heart" is about "cross-cultural understanding and the values that people of all faiths share. This is not a film about terrorism or conflict, it is a story of people of all faiths working together to find the truth."
Pune, a metropolitan area with more than 4 million people, is in Maharashtra state, about 80 miles (130 km) southeast of Mumbai.