Rosenthal died of natural causes at an assisted living facility in the San Francisco suburb of Novato, said his daughter, Anne Rosenthal.
"He was a good and honest man, he had real integrity," she said.
Rosenthal's iconic photo, shot on Feb. 23, 1945, became the model for the Iwo Jima Memorial near Arlington National Cemetery in Virginia. The memorial, dedicated in 1954 and known officially as the Marine Corps War Memorial, commemorates the Marines who died taking the Pacific island in World War II.
The photo was listed in 1999 at No. 68 on a New York University survey of 100 examples of the best journalism of the century.
It shows the second raising of the flag that day on Mount Suribachi on the Japanese island. The first flag had been deemed too small.
"What I see behind the photo is what it took to get up to those heights — the kind of devotion to their country that those young men had, and the sacrifices they made," Rosenthal once said. "I take some gratification in being a little part of what the U.S. stands for."
He liked to call himself "a guy who was up in the big leagues for a cup of coffee at one time."
The picture was an inspiration for Thomas E. Franklin of The Record of Bergen County, N.J., who took the photo of three firefighters raising a flag amid the ruins of the World Trade Center on Sept. 11, 2001. Franklin said he instantly saw the similarities with the Iwo Jima photo as he looked through his lens. Franklin's photo, distributed worldwide by the AP, was a finalist in 2002 for the Pulitzer Prize in breaking news photography.
The small island of Iwo Jima was a strategic piece of land 750 miles south of Tokyo, and the United States wanted it to support long-range B-29 bombers and a possible invasion of Japan.
On Feb. 19, 1945, 30,000 Marines landed on the southeast coast. Mount Suribachi, at 546 feet the highest point on the island, took four days for the troops to scale. In all, more than 6,800 U.S. servicemen died in the five-week battle for the island, and the 21,000-man Japanese defense force was virtually wiped out.
Ten years after the flag-raising, Rosenthal wrote that he almost didn't go up to the summit when he learned a flag had already been raised. He decided to up anyway, and found servicemen preparing to put up the second, larger flag.
"Out of the corner of my eye, I had seen the men start the flag up. I swung my camera and shot the scene. That is how the picture was taken, and when you take a picture like that, you don't come away saying you got a great shot. You don't know."
"Millions of Americans saw this picture five or six days before I did, and when I first heard about it, I had no idea what picture was meant."
He recalled that days later, when a colleague congratulated him on the picture, he thought he meant another, posed shot he had taken later that day, of Marines waving and cheering at the base of the flag.
He added that if he had posed the flag-raising picture, as some skeptics have suggested over the years, "I would, of course, have ruined it" by choosing fewer men and making sure their faces could be seen.
Standing near Rosenthal was Marine Sgt. Bill Genaust, the motion picture cameraman who filmed the same flag-raising. He was killed in combat just days later. A frame of Genaust's film is nearly identical to the Rosenthal photo.
The AP photo quickly became the subject of posters, war-bond drives and a U.S. postage stamp.
Rosenthal left the AP later in 1945 to join the San Francisco Chronicle, where he worked as a photographer for 35 years before retiring.
"He was short in stature but that was about it. He had a lot of nerve," said John O'Hara, a retired photographer who worked with Rosenthal at the San Francisco Chronicle.
O'Hara said Rosenthal took special pride in a certificate naming him an honorary Marine and remained spry and alert well into his 90s.
Rosenthal's famous picture kept him busy for years, and he continued to get requests for prints decades after the shutter clicked. He said he was always flattered by the tumult surrounding the shot, but added, "I'd rather just lie down and listen to a ball game."
"He was the best photographer," said friend and fellow Pulitzer Prize winning photographer Nick Ut of The Associated Press, who said he spoke with Rosenthal last week. "His picture no one forgets. People know the photo very well."
Ut's 1972 image of a little girl, naked and screaming in agony as she flees a napalm bomb attack during the Vietnam War, stoked anti-war sentiment. But Rosenthal's photo helped fuel patriotism in the United States.
"People say to me, yours is so sad. You see his picture and it shows how Americans won the war," Ut said.
Rosenthal was born in 1911 in Washington, D.C.
He took up photography as a hobby. As the Depression got under way, Rosenthal moved to San Francisco, living with a brother until he found a job with the Newspaper Enterprise Association in 1930.
In 1932, Rosenthal joined the old San Francisco News as a combination reporter and photographer.
"They just told me to take this big box and point the end with the glass toward the subject and press the shutter and `We'll tell you what you did wrong,"' he said.
After a short time with ACME Newspictures in San Francisco in 1936, Rosenthal became San Francisco bureau chief of The New York Times-Wide World Photos.
Rosenthal began working for the AP in San Francisco when the news cooperative bought Wide World Photos. After a stint in the Merchant Marine, he returned to the AP and was sent to cover battle areas in 1944.
His first assignment was in New Guinea, and he also covered the invasion of Guam before making his famous photo on Iwo Jima.
In addition to his daughter, Rosenthal is survived by his ex-wife Lee Rosenthal, his son Joseph J. Rosenthal Jr., and their families.