The Navy did not provide a cause of death but said he was suffering from Alzheimer's disease. He died at his home in Coronado, Calif.
In the 1992 presidential election, Stockdale became independent candidate Perot's vice presidential running mate, initially as a stand-in on the ticket but later as the candidate.
Stockdale gave a stumbling performance in the nationally televised vice-presidential debate against Dan Quayle and Al Gore and later said he didn't feel comfortable in the public eye.
During the debate, he commented on an exchange between Quayle and Gore:
"I think America is seeing right now the reason this nation is in gridlock. The trickle-downs and the tax-and-spends, or whatever you want to call them, are at swords point."
When Perot ran again in 1996 as the candidate of his Reform Party, Stockdale had rejoined the Republican Party.
Stockdale was born in Abingdon, Ill., and graduated from the U.S. Naval Academy in 1947.
During the Vietnam War, he was a Navy fighter pilot based on the USS Oriskany and flew 201 missions before he was shot down on Sept. 9, 1965. He became the highest-ranking naval officer captured during the war, the Navy said.
He endured more than seven-and-a-half years as a prisoner, spending four of them in solitary confinement, before his release in 1973. He was tortured repeatedly, according to the Navy.
Stockdale received 26 combat decorations, including the Medal of Honor, the nation's highest medal for valor, in 1976. A portion of his award citation reads: "Stockdale ... deliberately inflicted a near mortal wound to his person in order to convince his captors of his willingness to give up his life rather than capitulate. He was subsequently discovered and revived by the North Vietnamese who, convinced of his indomitable spirit, abated their employment of excessive harassment and torture of all prisoners of war."
He retired from the military in 1979.
Survivors include his wife, Sybil, and four sons.