Thompson, whose role in the 1968 massacre did not become widely known until decades later, died at the Veterans Affairs Medical Center in Alexandria, hospital spokesman Jay DeWorth said.
Trent Angers, Thompson's biographer and family friend, said Thompson died of cancer.
"These people were looking at me for help and there was no way I could turn my back on them," Thompson recalled in a 1998 Associated Press interview.
Early in the morning of March 16, 1968, Thompson, door-gunner Lawrence Colburn and crew chief Glenn Andreotta came upon U.S. ground troops killing Vietnamese civilians in and around the village of My Lai.
They landed the helicopter in the line of fire between American troops and fleeing Vietnamese civilians and pointed their own guns at the U.S. soldiers to prevent more killings.
Colburn and Andreotta had provided cover for Thompson as he went forward to confront the leader of the U.S. forces. Thompson later coaxed civilians out of a bunker so they could be evacuated, and then landed his helicopter again to pick up a wounded child they transported to a hospital. Their efforts led to the cease-fire order at My Lai.
In 1998, the Army honored the three men with the prestigious Soldier's Medal, the highest award for bravery not involving conflict with an enemy. It was a posthumous award for Andreotta, who had been killed in battle three weeks after My Lai.
"It was the ability to do the right thing even at the risk of their personal safety that guided these soldiers to do what they did," Army Maj. Gen. Michael Ackerman said at the 1998 ceremony. The three "set the standard for all soldiers to follow."
Lt. William L. Calley, a platoon leader, was convicted and sentenced to life imprisonment for his role in the killings, but served just three years under house arrest when then-President Nixon reduced his sentence.
Author Seymour Hersh won the 1970 Pulitzer Prize for his expose of the massacre in 1969 while working as a freelance journalist. The massacre became one of the pivotal events as opposition to the war was growing in the United States.
Hersh called Thompson "one of the good guys."
"You can't imagine what courage it took to do what he did," Hersh said.
Although Thompson's story was a significant part of Hersh's reports, and Thompson testified before Congress, his role in ending My Lai wasn't widely known until the late 1980s, when David Egan, a professor emeritus at Clemson University, saw an interview in a documentary and launched a letter-writing campaign that eventually led to the awarding of the medals in 1998.
"He was the guy who by his heroic actions gave a morality and dignity to the American military effort," Tulane history professor Douglas Brinkley said.
For years Thompson suffered snubs and worse from those who considered him unpatriotic. He recalled a congressman angrily saying that Thompson himself was the only serviceman who should be punished because of My Lai.
As the years passed, Thompson became an example for future generations of soldiers, said Col. Tom Kolditz, head of the U.S. Military Academy's behavioral sciences and leadership department. Thompson went to West Point once a year to give a lecture on his experience, Kolditz said.
"There are so many people today walking around alive because of him, not only in Vietnam, but people who kept their units under control under other circumstances because they had heard his story. We may never know just how many lives he saved."